Soybean variety XR31C09

ABSTRACT

According to the invention, there is provided a novel soybean variety designated XR31C09. This invention thus relates to the seeds of soybean variety XR31C09, to the plants of soybean XR31C09 to plant parts of soybean variety XR31C09 and to methods for producing a soybean plant produced by crossing plants of the soybean variety XR31C09 with another soybean plant, using XR31C09 as either the male or the female parent.

FIELD OF INVENTION

This invention relates generally the field of soybean breeding,specifically relating to a soybean variety designated XR31C09.

BACKGROUND OF INVENTION

The present invention relates to a new and distinctive soybean variety,designated XR31C09 which has been the result of years of carefulbreeding and selection as part of a soybean breeding program. There arenumerous steps in the development of any novel, desirable plantgermplasm. Plant breeding begins with the analysis and definition ofproblems and weaknesses of the current germplasm, the establishment ofprogram goals, and the definition of specific breeding objectives. Thenext step is selection of germplasm that possess the traits to meet theprogram goals. The goal is to combine in a single variety an improvedcombination of desirable traits from the parental germplasm. Theseimportant traits may include but are not limited to higher seed yield,resistance to diseases and insects, tolerance to drought and heat,altered fatty acid profile, abiotic stress tolerance, improvements incompositional traits and better agronomic qualities.

These processes, which lead to the final step of marketing anddistribution, can take from six to twelve years from the time the firstcross is made. Therefore, development of new varieties is atime-consuming process that requires precise forward planning, efficientuse of resources, and a minimum of changes in direction.

Soybean (Glycine max), is an important and valuable field crop. Thus, acontinuing goal of soybean breeders is to develop stable, high yieldingsoybean varieties that are agronomically sound. The reasons for thisgoal are to maximize the amount of grain produced on the land used andto supply food for both animals and humans. To accomplish this goal, thesoybean breeder must select and develop soybean plants that have thetraits that result in superior varieties.

Pioneer soybean research staff create over 500,000 potential newvarieties each year. Of those new varieties, less than 50 and morecommonly less than 25 are actually selected for commercial use.

The soybean is the world's leading source of vegetable oil and proteinmeal. The oil extracted from soybeans is used for cooking oil,margarine, and salad dressings. Soybean oil is composed of saturated,monounsaturated and polyunsaturated fatty acids. It has a typicalcomposition of 11% palmitic, 4% stearic, 25% oleic, 50% linoleic and 9%linolenic fatty acid content (“Economic Implications of Modified SoybeanTraits Summary Report”, Iowa Soybean Promotion Board & American SoybeanAssociation Special Report 92S, May 1990). Changes in fatty acidcomposition for improved oxidative stability and nutrition are alsoimportant traits. Industrial uses for processed soybean oil includeingredients for paints, plastics, fibers, detergents, cosmetics, andlubricants. Soybean oil may be split, inter-esterified, sulfurized,epoxidized, polymerized, ethoxylated, or cleaved. Designing andproducing soybean oil derivatives with improved functionality,oliochemistry, is a rapidly growing field. The typical mixture oftriglycerides is usually split and separated into pure fatty acids,which are then combined with petroleum-derived alcohols or acids,nitrogen, sulfonates, chlorine, or with fatty alcohols derived from fatsand oils.

Soybean is also used as a food source for both animals and humans.Soybean is widely used as a source of protein for animal feeds forpoultry, swine and cattle. During processing of whole soybeans, thefibrous hull is removed and the oil is extracted. The remaining soybeanmeal is a combination of carbohydrates and approximately 50% protein.

For human consumption soybean meal is made into soybean flour which isprocessed to protein concentrates used for meat extenders or specialtypet foods. Production of edible protein ingredients from soybean offersa healthy, less expensive replacement for animal protein in meats aswell as dairy-type products.

SUMMARY OF INVENTION

According to the invention, there is provided a novel soybean variety,designated XR31C09. This invention thus relates to the seeds of soybeanvariety XR31C09, to the plants of soybean XR31C09, to plant parts ofsoybean variety XR31C09 and to methods for producing a soybean plantproduced by crossing soybean variety XR31C09 with another soybean plant,using XR31C09 as either the male or the female parent. This inventionalso relates to methods for introgressing a transgenic or mutant traitinto soybean variety XR31C09 and to the soybean plants and plant partsproduced by those methods. This invention also relates to soybeanvarieties or breeding varieties and plant parts derived from soybeanvariety XR31C09, to methods for producing other soybean varieties orplant parts derived from soybean variety XR31C09 and to the soybeanplants, varieties, and their parts derived from use of those methods.This invention further relates to soybean seeds, plants, and plant partsproduced by crossing the soybean variety XR31C09 with another soybeanvariety.

DEFINITIONS

Certain definitions used in the specification are provided below. Alsoin the examples which follow, a number of terms are used. In order toprovide a clear and consistent understanding of the specification andclaims, the following definitions are provided:

AERIAL WEB BLIGHT. Tolerance to Aerial Web Blight is rated on a scale of1 to 9, with a score of 1 being very susceptible ranging up to a scoreof 9 being tolerant.

ALLELE. Any of one or more alternative forms of a genetic sequence. In adiploid cell or organism, the two alleles of a given sequence typicallyoccupy corresponding loci on a pair of homologous chromosomes.

ALTER. The utilization of up-regulation, down-regulation, or genesilencing.

ANTHESIS. The time of a flower's opening.

APHID ANTIBIOSIS. Aphid antibiosis is the ability of a variety to reducethe survival, growth, or reproduction of aphids that feed on it.Screening scores are based on the ability of the plant to decrease therate of aphid reproduction. Plants are compared to resistant andsusceptible check plant grown in the same test. Scores of three=belowaverage, 5=average, 7=above average and 9=exceptional.

BACKCROSSING. Process in which a breeder crosses a progeny variety backto one of the parental genotypes one or more times. Backcrossing can beused to introduce one or more locus conversions from one geneticbackground into another.

BREEDING. The genetic manipulation of living organisms.

BU/A=Bushels per Acre. The seed yield in bushels/acre is the actualyield of the grain at harvest.

Brown Stem Rot=BSR=Brown Stem Rot Tolerance. This is a visual diseasescore from 1 to 9 comparing all genotypes in a given test. The score isbased on leaf symptoms of yellowing and necrosis caused by brown stemrot. A score of 9 indicates no symptoms. Visual scores range down to ascore of 1 which indicates severe symptoms of leaf yellowing andnecrosis.

BSRLF=Brown Stem Rot disease rating based solely on leaf diseasesymptoms. This is a visual disease score from 1 to 9 comparing allgenotypes in a given test. A score of 9 indicates no symptoms. Visualscores range down to a score of 1 which indicates severe symptoms.

BSRSTM=Brown Stem Rot disease rating based solely on stem diseasesymptoms. This is a visual disease score from 1 to 9 comparing allgenotypes in a given test. A score of 9 indicates no symptoms. Visualscores range down to a score of 1 which indicates severe symptoms.

CELL. Cell as used herein includes a plant cell, whether isolated, intissue culture or incorporated in a plant or plant part.

CHARCOAL ROT DISEASE. A fungal disease that is enhanced by hot and dryconditions, especially during reproductive growth stages. Score is basedon observations of the comparative ability to tolerate drought and limitlosses from charcoal rot infection among various soybean varieties.

CHLORIDE SENSITIVITY. This is a measure of the chloride concentration inthe plant tissue from 1 to 9. The higher the score the lower theconcentration of chloride concentration in the tissue measured.

CW or Canopy Width. This is visual observation of the canopy width from1 to 9 comparing all genotypes in a given test. 9=extremely bushy and1=very narrow.

CNKR or Stem Canker Tolerance. This is a visual disease score from 1 to9 comparing all genotypes in a given field test. The score is based uponfield reaction to the disease. A score of 9 indicates resistance to thedisease, whereas a score of 1 indicates the line is susceptible to thedisease.

STEM CANKER GENE. Resistance based on specific gene that infers specificresistance or susceptibility to a specific race of Stem Canker. Scoresof nine=high degree of resistance, 5=provides moderate resistance, 1=nospecific gene for resistance. This score is based upon a reaction oftooth pick inoculation. A score of 9 indicates no symptoms, whereas ascore of 1 indicates experimental unit showed lesions relative toresistant and susceptible checks within the test.

COTYLEDON. A cotyledon is a type of seed leaf. The cotyledon containsthe food storage tissues of the seed.

CROSS-POLLINATION. Fertilization by the union of two gametes fromdifferent plants.

DIPLOID. A cell or organism having two sets of chromosomes.

ELITE VARIETY. A variety that is sufficiently homozygous and homogeneousto be used for commercial grain production. An elite variety may also beused in further breeding.

EMBRYO. The embryo is the small plant contained within a mature seed.

EMGSC=Field Emergence=Emergence Score. A score based upon speed andstrength of emergence at sub-optimal conditions. Rating occurs atunifoliate to first trifoliate. A score from 1 to 9 scale is given, with9 being the best and 1 the poorest. 9, 8, 7-degrees of optimal stands;vigorous growth and plant health; 6, 5, 4-degrees of less than optimalstands; moderate growth and plant health; 3, 2, 1-degrees ofunacceptable stands (potential replant situations); slow growth and poorplant health.

FEC=Iron-deficiency Chlorosis=Iron Chlorosis. Plants are scored 1 to 9based on visual observations. A score of 1 indicates the plants are deador dying from iron-deficiency chlorosis, a score of 5 means plants haveintermediate health with some leaf yellowing and a score of 9 means nostunting of the plants or yellowing of the leaves. Plots are usuallyscored in mid July.

FECL=Iron-deficiency Chlorosis. Plants are scored 1 to 9 based on visualobservations. A score of 1 indicates the plants are dead or dying fromiron-deficiency chlorosis, a score of 5 means plants have intermediatehealth with some leaf yellowing and a score of 9 means no stunting ofthe plants or yellowing of the leaves. Plots are scored around midAugust.

FEY or Frogeye Leaf Spot. This is a visual disease score from 1 to 9comparing all genotypes in a given test. The score is based upon leaflesions. A score of 9 indicates no lesions, whereas a score of 1indicates severe leaf necrosis.

FLOWER COLOR. Data values include: P=purple and W=white.

GENE SILENCING. The interruption or suppression of the expression of agene at the level of transcription or translation.

GENOTYPE. Refers to the genetic constitution of a cell or organism.

PLANT HABIT. This refers to the physical appearance of a plant. It canbe determinate (Det), semi-determinate, intermediate, or indeterminate(Ind). In soybeans, indeterminate varieties are those in which stemgrowth is not limited by formation of a reproductive structure (i.e.,flowers, pods and seeds) and hence growth continues throughout floweringand during part of pod filling. The main stem will develop and set podsover a prolonged period under favorable conditions. In soybeans,determinate varieties are those in which stem growth ceases at floweringtime. Most flowers develop simultaneously, and most pods fill atapproximately the same time. The terms semi-determinate and intermediateare also used to describe plant habit and are defined in Bernard, R. L.1972. “Two genes affecting stem termination in soybeans.” Crop Science12:235-239; Woodworth, C. M. 1932. “Genetics and breeding in theimprovement of the soybean.” Bull. Agric. Exp. Stn. (Illinois)384:297-404; Woodworth, C. M. 1933. “Genetics of the soybean.” J. Am.Soc. Agron. 25:36-51.

HAPLOID. A cell or organism having one set of the two sets ofchromosomes in a diploid.

HERBRES=Herbicide Resistance. This indicates that the plant is moretolerant to the herbicide shown than the level of herbicide toleranceexhibited by wild type plants. A designation of RR indicates toleranceto glyphosate and a designation of STS indicates tolerance tosulfonylurea herbicides.

HGT=Plant Height. Plant height is taken from the top of the soil to toppod of the plant and is measured in inches.

HILUM. This refers to the scar left on the seed which marks the placewhere the seed was attached to the pod prior to it (the seed) beingharvested. Hila Color—data values include BR=brown; TN=tan; Y=yellow;BL=black IB=Imperfect Black; BF=buff.

HYPL=Hypocotyl length=Hypocotyl Elongation. This score indicates theability of the seed to emerge when planted 3″ deep in sand pots and witha controlled temperature of 25° C. The number of plants that emerge eachday are counted. Based on this data, each genotype is given a 1 to 9score based on its rate of emergence and percent of emergence. A scoreof 9 indicates an excellent rate and percent of emergence, anintermediate score of 5 indicates average ratings and a 1 scoreindicates a very poor rate and percent of emergence.

HYPOCOTYL. A hypocotyl is the portion of an embryo or seedling betweenthe cotyledons and the root. Therefore, it can be considered atransition zone between shoot and root.

LDGSEV=Lodging Resistance=Harvest Standability. Lodging is rated on ascale of 1 to 9. A score of 9 indicates erect plants. A score of 5indicates plants are leaning at a 45° angle in relation to the groundand a score of 1 indicates plants are laying on the ground.

LEAFLETS. These are part of the plant shoot, and they manufacture foodfor the plant by the process of photosynthesis.

LINKAGE. Refers to a phenomenon wherein alleles on the same chromosometend to segregate together more often than expected by chance if theirtransmission was independent.

LINKAGE DISEQUILIBRIUM. Refers to a phenomenon wherein alleles tend toremain together in linkage groups when segregating from parents tooffspring, with a greater frequency than expected from their individualfrequencies.

LLC=Oil with three percent or less Linolenic acid is classified as lowlinolenic oil. Linolenic acid is one of the five most abundant fattyacids in soybean seeds. It is measured by gas chromatography and isreported as a percent of the total oil content.

LLE=Linoleic Acid Percent. Linoleic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

LLN=Linolenic Acid Percent. Linolenic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

LOCUS. A defined segment of DNA.

PRM Predicted Relative Maturity or Relative Maturity. Soybean maturitiesare divided into relative maturity groups (00, 0, I, II, III, IV . . . Xor 00, 0, 1, 2, 3, . . . 10). Within maturity are sub-groups. Asub-group is a tenth of a relative maturity group (for example 1.3 wouldindicate a group 1 and subgroup 3).

MAT ABS=Absolute Maturity. This term is defined as the length of timefrom planting to complete physiological development (maturity). Theperiod from planting until maturity is reached is measured in days,usually in comparison to one or more standard varieties. Plants areconsidered mature when 95% of the pods have reached their mature color.

MATURITY GROUP. This refers to an agreed-on industry division of groupsof varieties, based on the zones in which they are adapted primarilyaccording to day length or latitude. They consist of very long daylength varieties (Groups 000, 00, 0), and extend to very short daylength varieties (Groups VII, VIII, IX, X).

Narrow rows. Term indicates 7″ and 15″ row spacing.

NEI DISTANCE. A quantitative measure of percent similarity between twolines. Nei's distance between lines A and B can be defined as1-(2*number alleles in common/(number alleles in A+number alleles in B).For example, if lines A and B are the same for 95 out of 100 alleles,the Nei distance would be 0.05. If lines A and B are the same for 98 outof 100 alleles, the Nei distance would be 0.02. Free software forcalculating Nei distance is available on the internet at multiplelocations such as, for example, at:evolution.genetics.washington.edu/phylip.html. See Nei, Proc Natl AcadSci, 76:5269-5273 (1979) which is incorporated by reference for thispurpose.

NUCLEIC ACID. An acidic, chainlike biological macromolecule consistingof multiple repeat units of phosphoric acid, sugar and purine andpyrimidine bases.

OIL=Oil Percent. Soybean seeds contain a considerable amount of oil. Oilis measured by NIR spectrophotometry, and is reported on an as ispercentage basis.

Oil/Meal TYPE: Designates varieties specially developed with thefollowing oil traits: HLC=High Oleic oil; LLC=Low Linolenic (3%linolenic content); ULC=Ultra Low Linolenic oil (1% linolenic oilcontent); HSC=High Sucrose meal; LPA=Low Phytic Acid; LST=Low Saturateoil; Blank=Conventional variety/oil composition.

OLC=Oleic Acid Percent. Oleic acid is one of the five most abundantfatty acids in soybean seeds. It is measured by gas chromatography andis reported as a percent of the total oil content.

PEDIGREE DISTANCE. Relationship among generations based on theirancestral links as evidenced in pedigrees. May be measured by thedistance of the pedigree from a given starting point in the ancestry.

PERCENT IDENTITY. Percent identity as used herein refers to thecomparison of the homozygous alleles of two soybean varieties. Percentidentity is determined by comparing a statistically significant numberof the homozygous alleles of two developed varieties. For example, apercent identity of 90% between soybean variety 1 and soybean variety 2means that the two varieties have the same allele at 90% of their loci.

PERCENT SIMILARITY. Percent similarity as used herein refers to thecomparison of the homozygous alleles of a soybean variety such asXR31C09 with another plant, and if the homozygous allele of XR31C09matches at least one of the alleles from the other plant then they arescored as similar. Percent similarity is determined by comparing astatistically significant number of loci and recording the number ofloci with similar alleles as a percentage. A percent similarity of 90%between XR31C09 and another plant means that XR31C09 matches at leastone of the alleles of the other plant at 90% of the loci.

PLANT. As used herein, the term “plant” includes reference to animmature or mature whole plant, including a plant from which seed orgrain or anthers have been removed. Seed or embryo that will produce theplant is also considered to be the plant.

PLANT PARTS. As used herein, the term “plant parts” includes leaves,stems, roots, root tips, anthers, seed, grain, embryo, pollen, ovules,flowers, cotyledon, hypocotyl, pod, flower, shoot and stalk, tissue,cells and the like.

PLM or Palmitic Acid Percent. Palmitic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

PMG infested soils: soils containing Phytophthora sojae.

POD. This refers to the fruit of a soybean plant. It consists of thehull or shell (pericarp) and the soybean seeds. Pod Color data valuesinclude: BR=brown; TN=tan.

PRT or Phytophthora Field Tolerance. Tolerance to Phytophthora root rotis rated on a scale of 1 to 9, with a score of 9 being the best orhighest tolerance ranging down to a score of 1 which indicates theplants have no tolerance to Phytophthora.

PHYTOPHTHORA RESISTANCE GENE. (−) no specific gene for resistance;1a=resistance to races 1-2, 10-11, 13-8, 24; lc=resistance to races 1-3,6-11, 13, 15, 17, 21, 23, 24, 26, 28-30, 32, 34, 36. 1 k=resistance toraces 1-11, 13-15, 17, 18, 21-24, 26, 36, 37.; 6=resistance to races1-4, 10, 12, 14-16, 18-21, 25, 28, 33-35.

PRMMAT or Predicted Relative Maturity. Soybean maturities are dividedinto relative maturity groups. In the United States the most commonmaturity groups are 00 through VIII. Within maturity groups 00 through Vare sub-groups. A sub-group is a tenth of a relative maturity group.Within narrow comparisons, the difference of a tenth of a relativematurity group equates very roughly to a day difference in maturity atharvest.

PRO or Protein Percent. Soybean seeds contain a considerable amount ofprotein. Protein is generally measured by NIR spectrophotometry, and isreported on a dry weight basis.

PUBESCENCE. This refers to a covering of very fine hairs closelyarranged on the leaves, stems and pods of the soybean plant. PubescenceColor-data values include: L=Light Tawny; T=Tawny; G=Gray.

R160 or Palmitic Acid percentage. Percentage of palmitic acid asdetermined using methods described in Reske, et al., TriacylglycerolComposition and Structure in Genetically Modified Sunflower and SoybeanOils. JAOCS 74:8, 989-998 (1997), which is incorporated by reference forthis purpose.

R180 or Stearic acid percentage. Percentage of Stearic acid asdetermined using methods described in Reske, et al., TriacylglycerolComposition and Structure in Genetically Modified Sunflower and SoybeanOils. JAOCS 74:8, 989-998 (1997), which is incorporated by reference forthis purpose.

R181 or Oleic acid percentage. Percentage of oleic acid as determinedusing methods described in Reske, et al., Triacylglycerol Compositionand Structure in Genetically Modified Sunflower and Soybean Oils. JAOCS74:8, 989-998 (1997), which is incorporated by reference for thispurpose.

R182 or Linoleic acid percentage. Percentage of linoleic acid asdetermined using methods described in Reske, et al., TriacylglycerolComposition and Structure in Genetically Modified Sunflower and SoybeanOils. JAOCS 74:8, 989-998 (1997), which is incorporated by reference forthis purpose.

R183 or Linolenic acid percentage. Percentage of linolenic acid asdetermined using methods described in Reske, et al., TriacylglycerolComposition and Structure in Genetically Modified Sunflower and SoybeanOils. JAOCS 74:8, 989-998 (1997), which is incorporated by reference forthis purpose.

RESISTANCE. Synonymous with tolerance. The ability of a plant towithstand exposure to an insect, disease, herbicide or other condition.A resistant plant variety will have a level of resistance higher than acomparable wild-type variety.

RKI or Root-knot Nematode, Southern. This is a visual disease score from1 to 9 comparing all genotypes in a given test. The score is based upondigging plants to visually score the roots for presence or absence ofgalling. A score of 9 indicates that there is no galling of the roots, ascore of 1 indicates large severe galling cover most of the root systemwhich results in pre-mature death from decomposing of the root system.

RKA or Root-knot Nematode, Peanut. This is a visual disease score from 1to 9 comparing all genotypes in a given test. The score is based upondigging plants to look at the roots for presence or absence of galling.A score of 9 indicates that there is no galling of the roots, a score of1 indicates large severe galling cover most of the root system whichresults in pre-mature death from decomposing of the root system.

SCN=Soybean Cyst Nematode Resistance=Cyst Nematode Resistance. The scoreis based on resistance to a particular race of soybean cyst nematode,such as race 1, 2, 3, 5 or 14. Scores are visual observations ofresistance as versus other genotypes in the test, with a higher scoreindicating a higher level of resistance.

SCN Resistance Source. There are three sources of genetic resistance toSCN: P188788, P1548402 (also known as Peking), and P1437654 (also knownas Hartwig).

SCN infected soils: soils containing soybean cyst nematode.

SD VIG or Seedling Vigor. The score is based on the speed of emergenceof the plants within a plot relative to other plots within anexperiment. A score of 9 indicates that 90% of plants growing haveexpanded first leaves. A score of 1 indicates no plants have expandedfirst leaves.

SDS or Sudden Death Syndrome. Tolerance to Sudden Death Syndrome israted on a scale of 1 to 9, with a score of 1 being very susceptibleranging up to a score of 9 being tolerant.

SEED COAT LUSTER. Data values include D=dull; S=shiny.

SEED SIZE SCORE. This is a measure of the seed size from 1 to 9. Thehigher the score the smaller the seed size measured.

SPLB=S/LB=Seeds per Pound. Soybean seeds vary in seed size, therefore,the number of seeds required to make up one pound also varies. Thisaffects the pounds of seed required to plant a given area, and can alsoimpact end uses.

SHATTR or Shattering. This refers to the amount of pod dehiscence priorto harvest. Pod dehiscence involves seeds falling from the pods to thesoil. This is a visual score from 1 to 9 comparing all genotypes withina given test. A score of 9 means pods have not opened and no seeds havefallen out and a score of 1 indicates 100% of the pods are opened.

SHOOTS. These are a portion of the body of the plant. They consist ofstems, petioles and leaves.

STC or Stearic Acid Percent. Stearic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

SUBLINE. Although XR31C09 contains substantially fixed genetics, and isphenotypically uniform and with no off-types expected, there stillremains a small proportion of segregating loci either within individualsor within the population as a whole. A breeder of ordinary skill in theart may fix these loci by making them more uniform in order to optimizethe performance of the variety. One example of this type of approach isdescribed in the “breeding bias” methods described in U.S. Pat. No.5,437,697 and U.S. patent application Ser. No. 10/901,425 may beutilized by a breeder of ordinary skill in the art to further purify thevariety in order to increase its yield. By sublining in this manner, nocrosses to a different variety are made, and so a new genetic variety isnot created and the overall genetic composition of the variety remainsessentially the same.

WH MD or White Mold Tolerance. This is a visual disease score from 1 to9 comparing all genotypes in a given test. The score is based uponobservations of mycelial growth and death of plants. A score of 9indicates no symptoms. Visual scores of 1 indicate complete death of theexperimental unit.

VARIETY. A substantially homozygous soybean line and minor modificationsthereof that retain the overall genetics of the soybean line includingbut not limited to a subline, a locus conversion, a mutation, atransgene, or a somaclonal variant.

High yield environments. Areas which lack normal stress for example theyhave sufficient rainfall, water drainage, low disease pressure, and lowweed pressure

Tough environments. Areas which have stress challenges, opposite of ahigh yield environment

DETAILED DESCRIPTION OF INVENTION

The variety of the invention has shown uniformity and stability for alltraits, as described in the following variety description information.It has been self-pollinated a sufficient number of generations, withcareful attention to uniformity of plant type to ensure a sufficientlevel of homozygosity and phenotypic stability. The variety has beenincreased with continued observation for uniformity. No variant traitshave been observed or are expected.

Strengths of Soybean variety XR31C09 include glyphosate resistance, higholeic acid content and low linolenic acid content (<3%).

There are few other varieties at this RM which have the yield potential,modified fatty acid profile and glyphosate resistance that XR31C09 has.

Soybean variety XR31C09 exhibits a relative maturity of 3 and a subgroupof approximately 1. A variety description of Soybean variety XR31C09 isprovided in Table 1. Traits reported are average values for alllocations and years or samples measured.

Soybean variety XR31C09, being substantially homozygous, can bereproduced by planting seeds of the variety, growing the resultingsoybean plants under self-pollinating or sib-pollinating conditions, andharvesting the resulting seed, using techniques familiar to theagricultural arts.

Performance Examples of XR31C09

In the examples in Table 2, the traits and characteristics of soybeanvariety XR31C09 are given in paired comparisons with the Pioneervarieties shown in the following tables. Traits reported are mean valuesfor all locations and years where paired comparison data was obtained.

Further Embodiments of the Invention Genetic Marker Profile Through SSRand First Generation Progeny

In addition to phenotypic observations, a plant can also be identifiedby its genotype. The genotype of a plant can be characterized through agenetic marker profile which can identify plants of the same variety ora related variety or be used to determine or validate a pedigree.Genetic marker profiles can be obtained by techniques such asRestriction Fragment Length Polymorphisms (RFLPs), Randomly AmplifiedPolymorphic DNAs (RAPDs), Arbitrarily Primed Polymerase Chain Reaction(AP-PCR), DNA Amplification Fingerprinting (DAF), Sequence CharacterizedAmplified Regions (SCARs), Amplified Fragment Length Polymorphisms(AFLPs), Simple Sequence Repeats (SSRs) which are also referred to asMicrosatellites, and Single Nucleotide Polymorphisms (SNPs). Forexample, see Cregan et. al, “An Integrated Genetic Linkage Map of theSoybean Genome” Crop Science 39:1464-1490 (1999), and Berry et al.,Assessing Probability of Ancestry Using Simple Sequence Repeat Profiles:Applications to Maize Inbred Lines and Soybean Varieties” Genetics165:331-342 (2003), each of which are incorporated by reference hereinin their entirety.

Particular markers used for these purposes are not limited to anyparticular set of markers, but are envisioned to include any type ofmarker and marker profile which provides a means of distinguishingvarieties. One method of comparison is to use only homozygous loci forXR31C09. For example, one set of publicly available markers which couldbe used to screen and identify variety XR31C09 is disclosed in Table 3.

Primers and PCR protocols for assaying these and other markers aredisclosed in the Soybase (sponsored by the USDA Agricultural ResearchService and Iowa State University) located at the world wide web at129.186.26.94/SSR.html. In addition to being used for identification ofsoybean variety XR31C09 and plant parts and plant cells of varietyXR31C09, the genetic profile may be used to identify a soybean plantproduced through the use of XR31C09 or to verify a pedigree for progenyplants produced through the use of XR31C09. The genetic marker profileis also useful in breeding and developing backcross conversions.

The present invention comprises a soybean plant characterized bymolecular and physiological data obtained from the representative sampleof said variety deposited with the ATCC. Further provided by theinvention is a soybean plant formed by the combination of the disclosedsoybean plant or plant cell with another soybean plant or cell andcomprising the homozygous alleles of the variety.

Means of performing genetic marker profiles using SSR polymorphisms arewell known in the art. SSRs are genetic markers based on polymorphismsin repeated nucleotide sequences, such as microsatellites. A markersystem based on SSRs can be highly informative in linkage analysisrelative to other marker systems in that multiple alleles may bepresent. Another advantage of this type of marker is that, through useof flanking primers, detection of SSRs can be achieved, for example, bythe polymerase chain reaction (PCR), thereby eliminating the need forlabor-intensive Southern hybridization. The PCR detection is done by useof two oligonucleotide primers flanking the polymorphic segment ofrepetitive DNA. Repeated cycles of heat denaturation of the DNA followedby annealing of the primers to their complementary sequences at lowtemperatures, and extension of the annealed primers with DNA polymerase,comprise the major part of the methodology.

Following amplification, markers can be scored by electrophoresis of theamplification products. Scoring of marker genotype is based on the sizeof the amplified fragment, which may be measured by the number of basepairs of the fragment. While variation in the primer used or inlaboratory procedures can affect the reported fragment size, relativevalues should remain constant regardless of the specific primer orlaboratory used. When comparing varieties it is preferable if all SSRprofiles are performed in the same lab.

Primers used are publicly available and may be found in the Soybase orCregan supra. See also, PCT Publication No. WO 99/31964 NucleotidePolymorphisms in Soybean, U.S. Pat. No. 6,162,967 Positional Cloning ofSoybean Cyst Nematode Resistance Genes, and US2002/0129402A1 SoybeanSudden Death Syndrome Resistant Soybeans and Methods of Breeding andIdentifying Resistant Plants, the disclosure of which are incorporatedherein by reference.

The SSR profile of soybean plant XR31C09 can be used to identify plantscomprising XR31C09 as a parent, since such plants will comprise the samehomozygous alleles as XR31C09. Because the soybean variety isessentially homozygous at all relevant loci, most loci should have onlyone type of allele present. In contrast, a genetic marker profile of anF1 progeny should be the sum of those parents, e.g., if one parent washomozygous for allele x at a particular locus, and the other parenthomozygous for allele y at that locus, then the F1 progeny will be xy(heterozygous) at that locus. Subsequent generations of progeny producedby selection and breeding are expected to be of genotype x (homozygous),y (homozygous), or xy (heterozygous) for that locus position. When theF1 plant is selfed or sibbed for successive filial generations, thelocus should be either x or y for that position.

In addition, plants and plant parts substantially benefiting from theuse of XR31C09 in their development, such as XR31C09 comprising abackcross conversion, transgene, or genetic sterility factor, may beidentified by having a molecular marker profile with a high percentidentity to XR31C09. Such a percent identity might be 95%, 96%, 97%,98%, 99%, 99.5% or 99.9% identical to XR31C09.

The SSR profile of XR31C09 also can be used to identify essentiallyderived varieties and other progeny varieties developed from the use ofXR31C09, as well as cells and other plant parts thereof. Such plants maybe developed using the markers identified in WO 00/31964, U.S. Pat. No.6,162,967 and US2002/0129402A1. Progeny plants and plant parts producedusing XR31C09 may be identified by having a molecular marker profile ofat least 25%, 30%, 35%, 40%, 45%, 50% /55%, 60%/65%, 70%,75%/76%/77%/78%/79%/80%, 81%/82%/83%, 84%/85%, 86%,87%/88%/89%/90%/91%/92%, 93%, 94%/95%, 96%, 97%, 98%, 99% or 99.5%genetic contribution from soybean variety, as measured by either percentidentity or percent similarity. Such progeny may be furthercharacterized as being within a pedigree distance of XR31C09, such aswithin 1,2,3,4 or 5 or less cross-pollinations to a soybean plant otherthan XR31C09, or a plant that has XR31C09 as a progenitor. Uniquemolecular profiles may be identified with other molecular tools such asSNPs and RFLPs.

Introduction of a New Trait or Locus into XR31C09

Variety XR31C09 represents a new base genetic variety into which a newlocus or trait may be introgressed. Direct transformation andbackcrossing represent two important methods that can be used toaccomplish such an introgression.

Backcross Conversions of XR31C09

A backcross conversion of XR31C09 occurs when DNA sequences areintroduced through backcrossing (Hallauer et al, 1988), with XR31C09utilized as the recurrent parent. Both naturally occurring andtransgenic DNA sequences may be introduced through backcrossingtechniques. A backcross conversion may produce a plant with a trait orlocus conversion in at least two or more backcrosses, including at least2 crosses, at least 3 crosses, at least 4 crosses, at least 5 crossesand the like. Molecular marker assisted breeding or selection may beutilized to reduce the number of backcrosses necessary to achieve thebackcross conversion. For example, see Openshaw, S. J. et al.,Marker-assisted Selection in Backcross Breeding. In: ProceedingsSymposium of the Analysis of Molecular Data, August 1994, Crop ScienceSociety of America, Corvallis, Oreg., where it is demonstrated that abackcross conversion can be made in as few as two backcrosses.

The complexity of the backcross conversion method depends on the type oftrait being transferred (single genes or closely linked genes as vs.unlinked genes), the level of expression of the trait, the type ofinheritance (cytoplasmic or nuclear) and the types of parents includedin the cross. It is understood by those of ordinary skill in the artthat for single gene traits that are relatively easy to classify, thebackcross method is effective and relatively easy to manage. (SeeHallauer et al. in Corn and Corn Improvement, Sprague and Dudley, ThirdEd. 1998). Desired traits that may be transferred through backcrossconversion include, but are not limited to, sterility (nuclear andcytoplasmic), fertility restoration, nutritional enhancements, droughttolerance, nitrogen utilization, altered fatty acid profile, lowphytate, industrial enhancements, disease resistance (bacterial, fungalor viral), insect resistance and herbicide resistance. In addition, anintrogression site itself, such as an FRT site, Lox site or other sitespecific integration site, may be inserted by backcrossing and utilizedfor direct insertion of one or more genes of interest into a specificplant variety. A single locus may contain several transgenes, such as atransgene for disease resistance that, in the same expression vector,also contains a transgene for herbicide resistance. The gene forherbicide resistance may be used as a selectable marker and/or as aphenotypic trait. A single locus conversion of site specific integrationsystem allows for the integration of multiple genes at the convertedloci.

The backcross conversion may result from either the transfer of adominant allele or a recessive allele. Selection of progeny containingthe trait of interest is accomplished by direct selection for a traitassociated with a dominant allele. Transgenes transferred viabackcrossing typically function as a dominant single gene trait and arerelatively easy to classify. Selection of progeny for a trait that istransferred via a recessive allele requires growing and selfing thefirst backcross generation to determine which plants carry the recessivealleles. Recessive traits may require additional progeny testing insuccessive backcross generations to determine the presence of the locusof interest. The last backcross generation is usually selfed to givepure breeding progeny for the gene(s) being transferred, although abackcross conversion with a stably introgressed trait may also bemaintained by further backcrossing to the recurrent parent withselection for the converted trait.

Along with selection for the trait of interest, progeny are selected forthe phenotype of the recurrent parent. The backcross is a form ofinbreeding, and the features of the recurrent parent are automaticallyrecovered after successive backcrosses. Poehlman, Breeding Field Crops,P. 204 (1987). Poehlman suggests from one to four or more backcrosses,but as noted above, the number of backcrosses necessary can be reducedwith the use of molecular markers. Other factors, such as a geneticallysimilar donor parent, may also reduce the number of backcrossesnecessary. As noted by Poehlman, backcrossing is easiest for simplyinherited, dominant and easily recognized traits.

One process for adding or modifying a trait or locus in soybean varietyXR31C09 comprises crossing XR31C09 plants grown from XR31C09 seed withplants of another soybean variety that comprise the desired trait orlocus, selecting F1 progeny plants that comprise the desired trait orlocus to produce selected F1 progeny plants, crossing the selectedprogeny plants with the XR31C09 plants to produce backcross progenyplants, selecting for backcross progeny plants that have the desiredtrait or locus and the morphological characteristics of soybean varietyXR31C09 to produce selected backcross progeny plants; and backcrossingto XR31C09 three or more times in succession to produce selected fourthor higher backcross progeny plants that comprise said trait or locus.The modified XR31C09 may be further characterized as having thephysiological and morphological characteristics of soybean varietyXR31C09 listed in Table 1 as determined at the 5% significance levelwhen grown in the same environmental conditions and/or may becharacterized by percent similarity or identity to XR31C09 as determinedby SSR markers. The above method may be utilized with fewer backcrossesin appropriate situations, such as when the donor parent is highlyrelated or markers are used in the selection step. Desired traits thatmay be used include those nucleic acids known in the art, some of whichare listed herein, that will affect traits through nucleic acidexpression or inhibition. Desired loci include the introgression of FRT,Lox and other sites for site specific integration, which may also affecta desired trait if a functional nucleic acid is inserted at theintegration site.

In addition, the above process and other similar processes describedherein may be used to produce first generation progeny soybean seed byadding a step at the end of the process that comprises crossing XR31C09with the introgressed trait or locus with a different soybean plant andharvesting the resultant first generation progeny soybean seed.

Transgenes

The advent of new molecular biological techniques has allowed theisolation and characterization of genetic elements with specificfunctions, such as encoding specific protein products. Scientists in thefield of plant biology developed a strong interest in engineering thegenome of plants to contain and express foreign genetic elements, oradditional, or modified versions of native or endogenous geneticelements in order to alter the traits of a plant in a specific manner.Any DNA sequences, whether from a different species or from the samespecies, which are inserted into the genome using transformation,backcrossing or other methods known to one of skill in the art arereferred to herein collectively as “transgenes”. Over the last fifteento twenty years several methods for producing transgenic plants havebeen developed, and the present invention also relates to transgenicvariants of the claimed soybean variety XR31C09.

One embodiment of the invention is a process for producing soybeanvariety XR31C09, further comprising a desired trait, said processcomprising transforming a soybean plant of variety XR31C09 with atransgene that confers a desired trait. Another embodiment is theproduct produced by this process. In one embodiment the desired traitmay be one or more of herbicide resistance, insect resistance, diseaseresistance, decreased phytate, or modified fatty acid or carbohydratemetabolism. The specific gene may be any known in the art or listedherein, including; a polynucleotide conferring resistance toimidazolinone, sulfonylurea, glyphosate, glufosinate, triazine andbenzonitrile; a polynucleotide encoding a bacillus thuringiensispolypeptide, a polynucleotide encoding phytase, FAD-2, FAD-3, galactinolsynthase or a raffinose synthetic enzyme; or a polynucleotide conferringresistance to soybean cyst nematode, brown stem rot, phytophthora rootrot, soybean mosaic virus or sudden death syndrome.

Numerous methods for plant transformation have been developed, includingbiological and physical plant transformation protocols. See, forexample, Miki et al., “Procedures for Introducing Foreign DNA intoPlants” in Methods in Plant Molecular Biology and Biotechnology, Glick,B. R. and Thompson, J. E. Eds. (CRC Press, Inc., Boca Raton, 1993) pages67-88 and Armstrong, “The First Decade of Maize Transformation: A Reviewand Future Perspective” (Maydica 44:101-109, 1999). In addition,expression vectors and in vitro culture methods for plant cell or tissuetransformation and regeneration of plants are available. See, forexample, Gruber et al., “Vectors for Plant Transformation” in Methods inPlant Molecular Biology and Biotechnology, Glick, B. R. and Thompson, J.E. Eds. (CRC Press, Inc., Boca Raton, 1993) pages 89-119.

The most prevalent types of plant transformation involve theconstruction of an expression vector. Such a vector comprises a DNAsequence that contains a gene under the control of or operatively linkedto a regulatory element, for example a promoter. The vector may containone or more genes and one or more regulatory elements.

A genetic trait which has been engineered into the genome of aparticular soybean plant may then be moved into the genome of anothervariety using traditional breeding techniques that are well known in theplant breeding arts. For example, a backcrossing approach is commonlyused to move a transgene from a transformed soybean variety into analready developed soybean variety, and the resulting backcrossconversion plant would then comprise the transgene(s).

Various genetic elements can be introduced into the plant genome usingtransformation. These elements include, but are not limited to genes;coding sequences; inducible, constitutive, and tissue specificpromoters; enhancing sequences; and signal and targeting sequences. Forexample, see the traits, genes and transformation methods listed in U.S.Pat. No. 6,118,055.

With transgenic plants according to the present invention, a foreignprotein can be produced in commercial quantities. Thus, techniques forthe selection and propagation of transformed plants, which are wellunderstood in the art, yield a plurality of transgenic plants that areharvested in a conventional manner, and a foreign protein then can beextracted from a tissue of interest or from total biomass. Proteinextraction from plant biomass can be accomplished by known methods whichare discussed, for example, by Heney and Orr, Anal. Biochem. 114:92-6(1981).

A genetic map can be generated, primarily via conventional RestrictionFragment Length Polymorphisms (RFLP), Polymerase Chain Reaction (PCR)analysis, Simple Sequence Repeats (SSR) and Single NucleotidePolymorphisms (SNP) that identifies the approximate chromosomal locationof the integrated DNA molecule. For exemplary methodologies in thisregard, see Glick and Thompson, METHODS IN PLANT MOLECULAR BIOLOGY ANDBIOTECHNOLOGY 269-284 (CRC Press, Boca Raton, 1993).

Wang et al. discuss “Large Scale Identification, Mapping and Genotypingof Single-Nucleotide Polymorphisms in the Human Genome”, Science,280:1077-1082, 1998, and similar capabilities are becoming increasinglyavailable for the soybean genome. Map information concerning chromosomallocation is useful for proprietary protection of a subject transgenicplant. If unauthorized propagation is undertaken and crosses made withother germplasm, the map of the integration region can be compared tosimilar maps for suspect plants to determine if the latter have a commonparentage with the subject plant. Map comparisons would involvehybridizations, RFLP, PCR, SSR and sequencing, all of which areconventional techniques. SNPs may also be used alone or in combinationwith other techniques.

Likewise, by means of the present invention, plants can be geneticallyengineered to express various phenotypes of agronomic interest. Throughthe transformation of soybean the expression of genes can be altered toenhance disease resistance, insect resistance, herbicide resistance,agronomic, grain quality and other traits. Transformation can also beused to insert DNA sequences which control or help controlmale-sterility. DNA sequences native to soybean as well as non-nativeDNA sequences can be transformed into soybean and used to alter levelsof native or non-native proteins. Various promoters, targetingsequences, enhancing sequences, and other DNA sequences can be insertedinto the genome for the purpose of altering the expression of proteins.Reduction of the activity of specific genes (also known as genesilencing, or gene suppression) is desirable for several aspects ofgenetic engineering in plants.

Many techniques for gene silencing are well known to one of skill in theart, including but not limited to knock-outs (such as by insertion of atransposable element such as mu (Vicki Chandler, The Maize Handbook ch.118 (Springer-Verlag 1994) or other genetic elements such as a FRT, Loxor other site specific integration site, antisense technology (see,e.g., Sheehy et al. (1988) PNAS USA 85:8805-8809; and U.S. Pat. Nos.5,107,065; 5,453,566; and 5,759,829); co-suppression (e.g., Taylor(1997) Plant Cell 9:1245; Jorgensen (1990) Trends Biotech.8(12):340-344; Flavell (1994) PNAS USA 91:3490-3496; Finnegan et al.(1994) Bio/Technology 12:883-888; and Neuhuber et al. (1994) Mol. Gen.Genet. 244:230-241); RNA interference (Napoli et al. (1990) Plant Cell2:279-289; U.S. Pat. No. 5,034,323; Sharp (1999) Genes Dev. 13:139-141;Zamore et al. (2000) Cell 101:25-33; and Montgomery et al. (1998) PNASUSA 95:15502-15507), virus-induced gene silencing (Burton, et al. (2000)Plant Cell 12:691-705; and Baulcombe (1999) Curr. Op. Plant Bio.2:109-113); target-RNA-specific ribozymes (Haseloff et al. (1988) Nature334: 585-591); hairpin structures (Smith et al. (2000) Nature407:319-320; WO 99/53050; and WO 98/53083); MicroRNA (Aukerman & Sakai(2003) Plant Cell 15:2730-2741); ribozymes (Steinecke et al. (1992) EMBOJ. 11:1525; and Perriman et al. (1993) Antisense Res. Dev. 3:253);oligonucleotide mediated targeted modification (e.g., WO 03/076574 andWO 99/25853); Zn-finger targeted molecules (e.g., WO 01/52620; WO03/048345; and WO 00/42219); and other methods or combinations of theabove methods known to those of skill in the art.

Exemplary nucleotide sequences that may be altered by geneticengineering include, but are not limited to, those categorized below.

1. Transgenes That Confer Resistance To Insects or Disease And ThatEncode:

(A) Plant disease resistance genes. Plant defenses are often activatedby specific interaction between the product of a disease resistance gene(R) in the plant and the product of a corresponding avirulence (Avr)gene in the pathogen. A plant variety can be transformed with clonedresistance gene to engineer plants that are resistant to specificpathogen strains. See, for example Jones et al., Science 266: 789 (1994)(cloning of the tomato Cf-9 gene for resistance to Cladosporium fulvum);Martin et al., Science 262:1432 (1993) (tomato Pto gene for resistanceto Pseudomonas syringae pv. tomato encodes a protein kinase); Mindrinoset al., Cell 78:1089 (1994) (Arabidopsis RSP2 gene for resistance toPseudomonas syringae), McDowell & Woffenden, (2003) Trends Biotechnol.21(4):178-83 and Toyoda et al., (2002) Transgenic Res. 11(6):567-82. Aplant resistant to a disease is one that is more resistant to a pathogenas compared to the wild type plant.

(B) A Bacillus thuringiensis protein, a derivative thereof or asynthetic polypeptide modeled thereon. See, for example, Geiser et al.,Gene 48:109 (1986), who disclose the cloning and nucleotide sequence ofa Btdelta-endotoxin gene. Moreover, DNA molecules encodingdelta-endotoxin genes can be purchased from American Type CultureCollection (Rockville, Md.), for example, under ATCC Accession Nos.40098, 67136, 31995 and 31998. Other non-limiting examples of Bacillusthuringiensis transgenes being genetically engineered are given in thefollowing patents and patent applications and hereby are incorporated byreference for this purpose: U.S. Pat. Nos. 5,188,960; 5,689,052;5,880,275; 5,986,177; 7,105,332; 7,208,474; WO 91/14778; WO 99/31248; WO01/12731; WO 99/24581; WO 97/40162 and U.S. application Ser. Nos.10/032,717; 10/414,637; 11/018,615; 11/404,297; 11/404,638; 11/471,878;11/780,501; 11/780,511; 11/780,503; 11/953,648; 11/953,648; and11/957,893.

(C) An insect-specific hormone or pheromone such as an ecdysteroid andjuvenile hormone, a variant thereof, a mimetic based thereon, or anantagonist or agonist thereof. See, for example, the disclosure byHammock et al., Nature 344:458 (1990), of baculovirus expression ofcloned juvenile hormone esterase, an inactivator of juvenile hormone.

(D) An insect-specific peptide which, upon expression, disrupts thephysiology of the affected pest. For example, see the disclosures ofRegan, J. Biol. Chem. 269:9 (1994) (expression cloning yields DNA codingfor insect diuretic hormone receptor); Pratt et al., Biochem. Biophys.Res. Comm. 163:1243 (1989) (an allostatin is identified in Diplopterapuntata); Chattopadhyay et al. (2004) Critical Reviews in Microbiology30(1): 33-54 2004; Zjawiony (2004) J Nat Prod 67(2): 300-310; Carlini &Grossi-de-Sa (2002) Toxicon, 40(11): 1515-1539; Ussuf et al. (2001) CurrSci. 80(7): 847-853; and Vasconcelos & Oliveira (2004) Toxicon44(4):385-403. See also U.S. Pat. No. 5,266,317 to Tomalski et al., whodisclose genes encoding insect-specific toxins.

(E) An enzyme responsible for a hyperaccumulation of a monterpene, asesquiterpene, a steroid, hydroxamic acid, a phenylpropanoid derivativeor another non-protein molecule with insecticidal activity.

(F) An enzyme involved in the modification, including thepost-translational modification, of a biologically active molecule; forexample, a glycolytic enzyme, a proteolytic enzyme, a lipolytic enzyme,a nuclease, a cyclase, a transaminase, an esterase, a hydrolase, aphosphatase, a kinase, a phosphorylase, a polymerase, an elastase, achitinase and a glucanase, whether natural or synthetic. See PCTApplication No. WO 93/02197 in the name of Scott et al., which disclosesthe nucleotide sequence of a callase gene. DNA molecules which containchitinase-encoding sequences can be obtained, for example, from the ATCCunder Accession Nos. 39637 and 67152. See also Kramer et al., InsectBiochem. Molec. Biol. 23: 691 (1993), who teach the nucleotide sequenceof a cDNA encoding tobacco hookworm chitinase, and Kawalleck et al.,Plant Molec. Biol. 21:673 (1993), who provide the nucleotide sequence ofthe parsley ubi4-2 polyubiquitin gene, and U.S. Pat. Nos. 6,563,020;7,145,060 and 7,087,810.

(G) A molecule that stimulates signal transduction. For example, see thedisclosure by Botella et al., Plant Molec. Biol. 24:757 (1994), ofnucleotide sequences for mung bean calmodulin cDNA clones, and Griess etal., Plant Physiol. 104:1467 (1994), who provide the nucleotide sequenceof a maize calmodulin cDNA clone.

(H) A hydrophobic moment peptide. See PCT Application No. WO 95/16776and U.S. Pat. No. 5,580,852 disclosure of peptide derivatives ofTachyplesin which inhibit fungal plant pathogens) and PCT ApplicationNo. WO 95/18855 and U.S. Pat. No. 5,607,914 (teaches syntheticantimicrobial peptides that confer disease resistance).

(I) A membrane permease, a channel former or a channel blocker. Forexample, see the disclosure by Jaynes et al., Plant Sci. 89: 43 (1993),of heterologous expression of a cecropin-beta lytic peptide analog torender transgenic tobacco plants resistant to Pseudomonas solanacearum.

(J) A viral-invasive protein or a complex toxin derived therefrom. Forexample, the accumulation of viral coat proteins in transformed plantcells imparts resistance to viral infection and/or disease developmenteffected by the virus from which the coat protein gene is derived, aswell as by related viruses. See Beachy et al., Ann. Rev. Phytopathol.28:451 (1990). Coat protein-mediated resistance has been conferred upontransformed plants against alfalfa mosaic virus, cucumber mosaic virus,tobacco streak virus, potato virus X, potato virus Y, tobacco etchvirus, tobacco rattle virus and tobacco mosaic virus. Id.

(K) An insect-specific antibody or an immunotoxin derived therefrom.Thus, an antibody targeted to a critical metabolic function in theinsect gut would inactivate an affected enzyme, killing the insect. Cf.Taylor et al., Abstract #497, SEVENTH INT'L SYMPOSIUM ON MOLECULARPLANT-MICROBE INTERACTIONS (Edinburgh, Scotland, 1994) (enzymaticinactivation in transgenic tobacco via production of single-chainantibody fragments).

(L) A virus-specific antibody. See, for example, Tavladoraki et al.,Nature 366:469 (1993), who show that transgenic plants expressingrecombinant antibody genes are protected from virus attack.

(M) A developmental-arrestive protein produced in nature by a pathogenor a parasite. Thus, fungal endo alpha-1,4-D-polygalacturonasesfacilitate fungal colonization and plant nutrient release bysolubilizing plant cell wall homo-alpha-1,4-D-galacturonase. See Lamb etal., Bio/Technology 10: 1436 (1992). The cloning and characterization ofa gene which encodes a bean endopolygalacturonase-inhibiting protein isdescribed by Toubart et al., Plant J. 2:367 (1992).

(N) A developmental-arrestive protein produced in nature by a plant. Forexample, Logemann et al., Bio/Technology 10:305 (1992), have shown thattransgenic plants expressing the barley ribosome-inactivating gene havean increased resistance to fungal disease.

(O) Genes involved in the Systemic Acquired Resistance (SAR) Responseand/or the pathogenesis related genes. Briggs, S., Current Biology, 5(2)(1995), Pieterse & Van Loon (2004) Curr. Opin. Plant Bio. 7(4):456-64and Somssich (2003) Cell 113(7):815-6.

(P) Antifungal genes (Cornelissen and Melchers, Pl. Physiol.101:709-712, (1993) and Parijs et al., Planta 183:258-264, (1991) andBushnell et al., Can. J. of Plant Path. 20(2):137-149 (1998). Also seeU.S. application Ser. Nos. 09/950,933; 11/619,645; 11/657,710;11/748,994; 11/774,121 and U.S. Pat. Nos. 6,891,085 and 7,306,946.

(Q) Detoxification genes, such as for fumonisin, beauvericin,moniliformin and zearalenone and their structurally related derivatives.For example, see U.S. Pat. Nos. 5,716,820; 5,792,931; 5,798,255;5,846,812; 6,083,736; 6,538,177; 6,388,171 and 6,812,380.

(R) Cystatin and cysteine proteinase inhibitors. See U.S. Pat. No.7,205,453.

(S) Defensin genes. See WO 03/000863 and U.S. Pat. Nos. 6,911,577;6,855,865; 6,777,592 and 7,238,781.

(T) Genes conferring resistance to nematodes. See e.g. PCT ApplicationWO 96/30517; PCT Application No. WO 93/19181, WO 03/033651 and Urwin etal., Planta 204:472-479 (1998), Williamson (1999) Curr Opin Plant Bio.2(4):327-31; and U.S. Pat. Nos. 6,284,948 and 7,301,069.

(U) Genes that confer resistance to Phytophthora Root Rot, such as theRps 1, Rps 1-a, Rps 1-b, Rps 1-c, Rps 1-d, Rps 1-e, Rps 1-k, Rps 2, Rps3-a, Rps 3-b, Rps 3-c, Rps 4, Rps 5, Rps 6, Rps 7 and other Rps genes.See, for example, Shoemaker et al, Phytophthora Root Rot Resistance GeneMapping in Soybean, Plant Genome IV Conference, San Diego, Calif.(1995).

(V) Genes that confer resistance to Brown Stem Rot, such as described inU.S. Pat. No. 5,689,035 and incorporated by reference for this purpose.

2. Transgenes That Confer Resistance To A Herbicide, For Example:

(A) A herbicide that inhibits the growing point or meristem, such as animidazolinone or a sulfonylurea. Exemplary genes in this category codefor mutant ALS and AHAS enzyme as described, for example, by Lee et al.,EMBO J. 7: 1241 (1988), and Miki et al., Theor. Appl. Genet. 80:449(1990), respectively. See also, U.S. Pat. Nos. 5,605,011; 5,013,659;5,141,870; 5,767,361; 5,731,180; 5,304,732; 4,761,373; 5,331,107;5,928,937; and 5,378,824; U.S. application Ser. No. 11/683,737, and PCTPublication No. WO 96/33270.

(B) Glyphosate (resistance imparted by mutant5-enolpyruvl-3-phosphikimate synthase (EPSP) and aroA genes,respectively) and other phosphono compounds such as glufosinate(phosphinothricin acetyl transferase (PAT) and Streptomyceshygroscopicus phosphinothricin acetyl transferase (bar) genes), andpyridinoxy or phenoxy proprionic acids and cyclohexones (ACCaseinhibitor-encoding genes). See, for example, U.S. Pat. No. 4,940,835 toShah et al., which discloses the nucleotide sequence of a form of EPSPSwhich can confer glyphosate resistance. U.S. Pat. No. 5,627,061 to Barryet al. also describes genes encoding EPSPS enzymes. See also U.S. Pat.Nos. 6,566,587; 6,338,961; 6,248,876 B1; 6,040,497; 5,804,425;5,633,435; 5,145,783; 4,971,908; 5,312,910; 5,188,642; 4,940,835;5,866,775; 6,225,114 B1; 6,130,366; 5,310,667; 4,535,060; 4,769,061;5,633,448; 5,510,471; Re. 36,449; RE 37,287 E; and 5,491,288; andinternational publications EP1173580; WO 01/66704; EP1173581 andEP1173582, which are incorporated herein by reference for this purpose.Glyphosate resistance is also imparted to plants that express a genethat encodes a glyphosate oxido-reductase enzyme as described more fullyin U.S. Pat. Nos. 5,776,760 and 5,463,175, which are incorporated hereinby reference for this purpose. In addition glyphosate resistance can beimparted to plants by the over expression of genes encoding glyphosateN-acetyltransferase. See, for example, U.S. application Ser. Nos.10/427,692; 10/835,615 and 11/507,751. A DNA molecule encoding a mutantaroA gene can be obtained under ATCC accession No. 39256, and thenucleotide sequence of the mutant gene is disclosed in U.S. Pat. No.4,769,061 to Comai. European Patent Application No. 0 333 033 to Kumadaet al. and U.S. Pat. No. 4,975,374 to Goodman et al. disclose nucleotidesequences of glutamine synthetase genes which confer resistance toherbicides such as L-phosphinothricin. The nucleotide sequence of aphosphinothricin-acetyl-transferase gene is provided in European PatentNo. 0 242 246 and 0 242 236 to Leemans et al. De Greef et al.,Bio/Technology 7: 61 (1989), describe the production of transgenicplants that express chimeric bar genes coding for phosphinothricinacetyl transferase activity. See also, U.S. Pat. Nos. 5,969,213;5,489,520; 5,550,318; 5,874,265; 5,919,675; 5,561,236; 5,648,477;5,646,024; 6,177,616 B1; and 5,879,903, which are incorporated herein byreference for this purpose. Exemplary genes conferring resistance tophenoxy proprionic acids and cyclohexones, such as sethoxydim andhaloxyfop, are the Acc1-S1, Acc1-S2 and Acc1-S3 genes described byMarshall et al., Theor. Appl. Genet. 83:435 (1992).

(C) A herbicide that inhibits photosynthesis, such as a triazine (psbAand gs+ genes) and a benzonitrile (nitrilase gene). Przibilla et al.,Plant Cell 3:169 (1991), describe the transformation of Chlamydomonaswith plasmids encoding mutant psbA genes. Nucleotide sequences fornitrilase genes are disclosed in U.S. Pat. No. 4,810,648 to Stalker, andDNA molecules containing these genes are available under ATCC AccessionNos. 53435, 67441 and 67442. Cloning and expression of DNA coding for aglutathione S-transferase is described by Hayes et al., Biochem. J. 285:173 (1992).

(D) Acetohydroxy acid synthase, which has been found to make plants thatexpress this enzyme resistant to multiple types of herbicides, has beenintroduced into a variety of plants (see, e.g., Hattori et al. (1995)Mol Gen Genet. 246:419). Other genes that confer resistance toherbicides include: a gene encoding a chimeric protein of rat cytochromeP4507A1 and yeast NADPH-cytochrome P450 oxidoreductase (Shiota et al.(1994) Plant Physiol 106:17), genes for glutathione reductase andsuperoxide dismutase (Aono et al. (1995)

Plant Cell Physiol 36:1687, and genes for various phosphotransferases(Datta et al. (1992) Plant Mol Biol 20:619).

(E) Protoporphyrinogen oxidase (protox) is necessary for the productionof chlorophyll, which is necessary for all plant survival. The protoxenzyme serves as the target for a variety of herbicidal compounds. Theseherbicides also inhibit growth of all the different species of plantspresent, causing their total destruction. The development of plantscontaining altered protox activity which are resistant to theseherbicides are described in U.S. Pat. Nos. 6,288,306 B1; 6,282,837 B1;and 5,767,373; and PCT Publication No. WO 01/12825.

3. Transgenes That Confer Or Contribute To an Altered GrainCharacteristic, Such As:

(A) Altered fatty acids, for example, by

(1) Down-regulation of stearoyl-ACP desaturase to increase stearic acidcontent of the plant. See Knultzon et al., Proc. Natl. Acad. Sci. USA89:2624 (1992) and WO 99/64579 (Genes for Desaturases to Alter LipidProfiles in Corn),

(2) Elevating oleic acid via FAD-2 gene modification and/or decreasinglinolenic acid via FAD-3 gene modification (see U.S. Pat. Nos.6,063,947; 6,323,392; 6,372,965 and WO 93/11245),

(3) Altering conjugated linolenic or linoleic acid content, such as inWO 01/12800,

(4) Altering LEC1, AGP, Dek1, Superal1, mi1ps, various Ipa genes such asIpa1, Ipa3, hpt or hggt. For example, see WO 02/42424, WO 98/22604, WO03/011015, U.S. Pat. No. 6,423,886, U.S. Pat. No. 6,197,561, U.S. Pat.No. 6,825,397, US2003/0079247, US2003/0204870, WO 02/057439, WO03/011015 and Rivera-Madrid, R. et al. Proc. Natl. Acad. Sci.92:5620-5624 (1995).

(B) Altered phosphorus content, for example, by the

-   -   (1) Introduction of a phytase-encoding gene would enhance        breakdown of phytate, adding more free phosphate to the        transformed plant. For example, see Van Hartingsveldt et al.,        Gene 127: 87 (1993), for a disclosure of the nucleotide sequence        of an Aspergillus niger phytase gene.    -   (2) Modulating a gene that reduces phytate content. In maize,        this, for example, could be accomplished, by cloning and then        re-introducing DNA associated with one or more of the alleles,        such as the LPA alleles, identified in maize mutants        characterized by low levels of phytic acid, such as in WO        05/113778 and/or by altering inositol kinase activity as in WO        02/059324, US2003/0009011, WO 03/027243, US2003/0079247, WO        99/05298, U.S. Pat. No. 6,197,561, U.S. Pat. No. 6,291,224, U.S.        Pat. No. 6,391,348, WO 02/059324, US2003/0079247, WO 98/45448,        WO 99/55882, WO 01/04147.    -   (C) Altered carbohydrates effected, for example, by altering a        gene for an enzyme that affects the branching pattern of starch        or, a gene altering thioredoxin such as NTR and/or TR^(x) (see.        (See U.S. Pat. No. 6,531,648 which is incorporated by reference        for this purpose) and/or a gamma zein knock out or mutant such        as cs27 or TUSC27 or en27 (See U.S. Pat. No. 6,858,778 and        US2005/0160488, US2005/0204418; which are incorporated by        reference for this purpose). See Shiroza et al., J. Bacteriol.        170:810 (1988) (nucleotide sequence of Streptococcus mutans        fructosyltransferase gene), Steinmetz et al., Mol. Gen. Genet.        200:220 (1985) (nucleotide sequence of Bacillus subtilis        levansucrase gene), Pen et al., Bio/Technology 10:292 (1992)        (production of transgenic plants that express Bacillus        lichenifonnis alpha-amylase), Elliot et al., Plant Molec. Biol.        21:515 (1993) (nucleotide sequences of tomato invertase genes),        Søgaard et al., J. Biol. Chem. 268:22480 (1993) (site-directed        mutagenesis of barley alpha-amylase gene), and Fisher et al.,        Plant Physiol. 102:1045 (1993) (maize endosperm starch branching        enzyme II), WO 99/10498 (improved digestibility and/or starch        extraction through modification of UDP-D-xylose 4-epimerase,        Fragile 1 and 2, Ref1, HCHL, C4H), U.S. Pat. No. 6,232,529        (method of producing high oil seed by modification of starch        levels (AGF)). The fatty acid modification genes mentioned        herein may also be used to affect starch content and/or        composition through the interrelationship of the starch and oil        pathways.

(D) Altered antioxidant content or composition, such as alteration oftocopherol or tocotrienols. For example, see U.S. Pat. No. 6,787,683,US2004/0034886 and WO 00/68393 involving the manipulation of antioxidantlevels, and WO 03/082899 through alteration of a homogentisate geranylgeranyl transferase (hggt).

(E) Altered essential seed amino acids. For example, see U.S. Pat. No.6,127,600 (method of increasing accumulation of essential amino acids inseeds), U.S. Pat. No. 6,080,913 (binary methods of increasingaccumulation of essential amino acids in seeds), U.S. Pat. No. 5,990,389(high lysine), WO 99/40209 (alteration of amino acid compositions inseeds), WO 99/29882 (methods for altering amino acid content ofproteins), U.S. Pat. No. 5,850,016 (alteration of amino acidcompositions in seeds), WO 98/20133 (proteins with enhanced levels ofessential amino acids), U.S. Pat. No. 5,885,802 (high methionine), U.S.Pat. No. 5,885,801 (high threonine), U.S. Pat. No. 6,664,445 (plantamino acid biosynthetic enzymes), U.S. Pat. No. 6,459,019 (increasedlysine and threonine), U.S. Pat. No. 6,441,274 (plant tryptophansynthase beta subunit), U.S. Pat. No. 6,346,403 (methionine metabolicenzymes), U.S. Pat. No. 5,939,599 (high sulfur), U.S. Pat. No. 5,912,414(increased methionine), WO 98/56935 (plant amino acid biosyntheticenzymes), WO 98/45458 (engineered seed protein having higher percentageof essential amino acids), WO 98/42831 (increased lysine), U.S. Pat. No.5,633,436 (increasing sulfur amino acid content), U.S. Pat. No.5,559,223 (synthetic storage proteins with defined structure containingprogrammable levels of essential amino acids for improvement of thenutritional value of plants), WO 96/01905 (increased threonine), WO95/15392 (increased lysine), US2003/0163838, US2003/0150014,US2004/0068767, U.S. Pat. No. 6,803,498, WO 01/79516.

4. Genes that Control Male-Sterility

There are several methods of conferring genetic male sterilityavailable, such as multiple mutant genes at separate locations withinthe genome that confer male sterility, as disclosed in U.S. Pat. Nos.4,654,465 and 4,727,219 to Brar et al. and chromosomal translocations asdescribed by Patterson in U.S. Pat. Nos. 3,861,709 and 3,710,511. Inaddition to these methods, Albertsen et al., U.S. Pat. No. 5,432,068,describe a system of nuclear male sterility which includes: identifyinga gene which is critical to male fertility; silencing this native genewhich is critical to male fertility; removing the native promoter fromthe essential male fertility gene and replacing it with an induciblepromoter; inserting this genetically engineered gene back into theplant; and thus creating a plant that is male sterile because theinducible promoter is not “on” resulting in the male fertility gene notbeing transcribed. Fertility is restored by inducing, or turning “on”,the promoter, which in turn allows the gene that confers male fertilityto be transcribed.

(A) Introduction of a deacetylase gene under the control of atapetum-specific promoter and with the application of the chemicalN-Ac-PPT (WO 01/29237).

(B) Introduction of various stamen-specific promoters (WO 92/13956, WO92/13957).

(C) Introduction of the barnase and the barstar gene (Paul et al. PlantMol. Biol. 19:611-622, 1992).

For additional examples of nuclear male and female sterility systems andgenes, see also, U.S. Pat. Nos. 5,859,341; 6,297,426; 5,478,369;5,824,524; 5,850,014; and 6,265,640; all of which are herebyincorporated by reference.

5. Genes that create a site for site specific DNA integration. Thisincludes the introduction of FRT sites that may be used in the FLP/FRTsystem and/or Lox sites that may be used in the Cre/Loxp system. Forexample, see Lyznik, et al., Site-Specific Recombination for GeneticEngineering in Plants, Plant Cell Rep (2003) 21:925-932 and WO 99/25821,which are hereby incorporated by reference. Other systems that may beused include the Gin recombinase of phage Mu (Maeser et al., 1991; VickiChandler, The Maize Handbook ch. 118 (Springer-Verlag 1994), the Pinrecombinase of E. coli (Enomoto et al., 1983), and the R/RS system ofthe pSRi plasmid (Araki et al., 1992).6. Genes that affect abiotic stress resistance (including but notlimited to flowering, ear and seed development, enhancement of nitrogenutilization efficiency, altered nitrogen responsiveness, droughtresistance or tolerance, cold resistance or tolerance, and saltresistance or tolerance) and increased yield under stress. For example,see: WO 00/73475 where water use efficiency is altered throughalteration of malate; U.S. Pat. Nos. 5,892,009, 5,965,705, 5,929,305,5,891,859, 6,417,428, 6,664,446, 6,706,866, 6,717,034, 6,801,104, WO00/060089, WO 01/026459, WO 00/1035725, WO 01/034726, WO 01/035727, WO00/1036444, WO 01/036597, WO 01/036598, WO 00/2015675, WO 02/017430, WO02/077185, WO 02/079403, WO 03/013227, WO 03/013228, WO 03/014327, WO04/031349, WO 04/076638, WO 98/09521, and WO 99/38977 describing genes,including CBF genes and transcription factors effective in mitigatingthe negative effects of freezing, high salinity, and drought on plants,as well as conferring other positive effects on plant phenotype;US2004/0148654 and WO 01/36596 where abscisic acid is altered in plantsresulting in improved plant phenotype such as increased yield and/orincreased tolerance to abiotic stress; WO 00/006341, WO 04/090143, U.S.application Ser. Nos. 10/817,483 and 09/545,334 where cytokininexpression is modified resulting in plants with increased stresstolerance, such as drought tolerance, and/or increased yield. Also seeWO 02/02776, WO 03/052063, JP2002281975, U.S. Pat. No. 6,084,153, WO01/64898, U.S. Pat. No. 6,177,275, and U.S. Pat. No. 6,107,547(enhancement of nitrogen utilization and altered nitrogenresponsiveness). For ethylene alteration, see US2004/0128719,US2003/0166197 and WO 00/32761. For plant transcription factors ortranscriptional regulators of abiotic stress, see e.g. US2004/0098764 orUS2004/0078852.

Other genes and transcription factors that affect plant growth andagronomic traits such as yield, flowering, plant growth and/or plantstructure, can be introduced or introgressed into plants, see e.g. WO97/49811 (LHY), WO 98/56918 (ESD4), WO 97/10339 and U.S. Pat. No.6,573,430 (TFL), U.S. Pat. No. 6,713,663 (FT), WO 96/14414 (CON), WO96/38560, WO 01/21822 (VRN1), WO 00/44918 (VRN2), WO 99/49064 (GI), WO00/46358 (FR1), WO 97/29123, U.S. Pat. No. 6,794,560, U.S. Pat. No.6,307,126 (GAI), WO 99/09174 (D8 and Rht), and WO 04/076638 and WO04/031349 (transcription factors).

Plant Breeding Techniques

Development of Soybean Sublines

Sublines of XR31C09 may also be developed. Although XR31C09 containssubstantially fixed genetics, and is phenotypically uniform and with nooff-types expected, there still remains a small proportion ofsegregating loci either within individuals or within the population as awhole. Sublining provides the ability to select for these loci, whichhave with no apparent morphological or phenotypic effect on the plantcharacteristics, but do have an affect on overall yield. For example,the “breeding bias” methods described in U.S. Pat. No. 5,437,697 andU.S. patent application Ser. No. 10/901,425 may be utilized by a breederof ordinary skill in the art to identify genetic loci that areassociated with yield potential to further purify the variety in orderto increase its yield. U.S. Pat. No. 5,437,697 and U.S. patentapplication Ser. No. 10/901,425 are incorporated by reference for thispurpose. Based on these teachings, a breeder of ordinary skill in theart may fix agronomically important loci by making them homozygous inorder to optimize the performance of the variety. No crosses to adifferent variety are made, and so a new genetic variety is not createdand the overall genetic composition of the variety remains essentiallythe same. The development of soybean sublines and the use of acceleratedyield technology is a plant breeding technique.

Using XR31C09 to Develop other Soybean Varieties

Soybean varieties such as XR31C09 are typically developed for use inseed and grain production. However, soybean varieties such as XR31C09also provide a source of breeding material that may be used to developnew soybean varieties. Plant breeding techniques known in the art andused in a soybean plant breeding program include, but are not limitedto, recurrent selection, mass selection, bulk selection, backcrossing,pedigree breeding, open pollination breeding, restriction fragmentlength polymorphism enhanced selection, genetic marker enhancedselection, making double haploids, and transformation. Oftencombinations of these techniques are used. The development of soybeanvarieties in a plant breeding program requires, in general, thedevelopment and evaluation of homozygous varieties. There are manyanalytical methods available to evaluate a new variety. The oldest andmost traditional method of analysis is the observation of phenotypictraits but genotypic analysis may also be used.

Using XR31C09 In a Breeding Program

This invention is directed to methods for producing a soybean plant bycrossing a first parent soybean plant with a second parent soybean plantwherein the first and/or second parent soybean plant is variety XR31C09.The other parent may be any soybean plant, such as a soybean plant thatis part of a synthetic or natural population. Any such methods usingsoybean variety XR31C09 are part of this invention: selfing, sibbing,backcrosses, mass selection, pedigree breeding, bulk selection, hybridproduction, crosses to populations, and the like. These methods are wellknown in the art and some of the more commonly used breeding methods aredescribed below. Descriptions of breeding methods can be found in one ofseveral reference books (e.g., Allard, Principles of Plant Breeding,1960; Simmonds, Principles of Crop Improvement, 1979; Sneep et al.,1979; Fehr, “Breeding Methods for Cultivar Development”, Chapter 7,Soybean Improvement, Production and Uses, 2^(nd) ed., Wilcox editor,1987).

Pedigree Breeding

Pedigree breeding starts with the crossing of two genotypes, such asXR31C09 and another soybean variety having one or more desirablecharacteristics that is lacking or which complements XR31C09. If the twooriginal parents do not provide all the desired characteristics, othersources can be included in the breeding population. In the pedigreemethod, superior plants are selfed and selected in successive filialgenerations. In the succeeding filial generations the heterozygouscondition gives way to homogeneous varieties as a result ofself-pollination and selection. Typically in the pedigree method ofbreeding, five or more successive filial generations of selfing andselection is practiced: F1→F2; F2→F3; F3→F4; F4→F₅, etc. After asufficient amount of inbreeding, successive filial generations willserve to increase seed of the developed variety. Preferably, thedeveloped variety comprises homozygous alleles at about 95% or more ofits loci.

In addition to being used to create a backcross conversion, backcrossingcan also be used in combination with pedigree breeding. As discussedpreviously, backcrossing can be used to transfer one or morespecifically desirable traits from one variety, the donor parent, to adeveloped variety called the recurrent parent, which has overall goodagronomic characteristics yet lacks that desirable trait or traits.However, the same procedure can be used to move the progeny toward thegenotype of the recurrent parent but at the same time retain manycomponents of the non-recurrent parent by stopping the backcrossing atan early stage and proceeding with selfing and selection. For example, asoybean variety may be crossed with another variety to produce a firstgeneration progeny plant. The first generation progeny plant may then bebackcrossed to one of its parent varieties to create a BC1 or BC2.Progeny are selfed and selected so that the newly developed variety hasmany of the attributes of the recurrent parent and yet several of thedesired attributes of the non-recurrent parent. This approach leveragesthe value and strengths of the recurrent parent for use in new soybeanvarieties.

Therefore, an embodiment of this invention is a method of making abackcross conversion of soybean variety XR31C09, comprising the steps ofcrossing a plant of soybean variety XR31C09 with a donor plantcomprising a desired trait, selecting an F1 progeny plant comprising thedesired trait, and backcrossing the selected F1 progeny plant to a plantof soybean variety XR31C09. This method may further comprise the step ofobtaining a molecular marker profile of soybean variety XR31C09 andusing the molecular marker profile to select for a progeny plant withthe desired trait and the molecular marker profile of XR31C09. In oneembodiment the desired trait is a mutant gene or transgene present inthe donor parent.

Recurrent Selection and Mass Selection

Recurrent selection is a method used in a plant breeding program toimprove a population of plants. XR31C09 is suitable for use in arecurrent selection program. The method entails individual plants crosspollinating with each other to form progeny. The progeny are grown andthe superior progeny selected by any number of selection methods, whichinclude individual plant, half-sib progeny, full-sib progeny and selfedprogeny. The selected progeny are cross pollinated with each other toform progeny for another population. This population is planted andagain superior plants are selected to cross pollinate with each other.Recurrent selection is a cyclical process and therefore can be repeatedas many times as desired. The objective of recurrent selection is toimprove the traits of a population. The improved population can then beused as a source of breeding material to obtain new varieties forcommercial or breeding use, including the production of a syntheticcultivar. A synthetic cultivar is the resultant progeny formed by theintercrossing of several selected varieties.

Mass selection is a useful technique when used in conjunction withmolecular marker enhanced selection. In mass selection seeds fromindividuals are selected based on phenotype or genotype. These selectedseeds are then bulked and used to grow the next generation. Bulkselection requires growing a population of plants in a bulk plot,allowing the plants to self-pollinate, harvesting the seed in bulk andthen using a sample of the seed harvested in bulk to plant the nextgeneration. Also, instead of self pollination, directed pollinationcould be used as part of the breeding program.

Mutation Breeding

Mutation breeding is another method of introducing new traits intosoybean variety XR31C09. Mutations that occur spontaneously or areartificially induced can be useful sources of variability for a plantbreeder. The goal of artificial mutagenesis is to increase the rate ofmutation for a desired characteristic. Mutation rates can be increasedby many different means including temperature, long-term seed storage,tissue culture conditions, radiation; such as X-rays, Gamma rays (e.g.cobalt 60 or cesium 137), neutrons, (product of nuclear fission byuranium 235 in an atomic reactor), Beta radiation (emitted fromradioisotopes such as phosphorus 32 or carbon 14), or ultravioletradiation (preferably from 2500 to 2900 nm), or chemical mutagens (suchas base analogues (5-bromo-uracil), related compounds (8-ethoxycaffeine), antibiotics (streptonigrin), alkylating agents (sulfurmustards, nitrogen mustards, epoxides, ethylenamines, sulfates,sulfonates, sulfones, lactones), azide, hydroxylamine, nitrous acid, oracridines. Once a desired trait is observed through mutagenesis thetrait may then be incorporated into existing germplasm by traditionalbreeding techniques. Details of mutation breeding can be found in“Principles of Cultivar Development” Fehr, 1993 Macmillan PublishingCompany. In addition, mutations created in other soybean plants may beused to produce a backcross conversion of XR31C09 that comprises suchmutation.

Breeding with Molecular Markers

Molecular markers, which includes markers identified through the use oftechniques such as Isozyme Electrophoresis, Restriction Fragment LengthPolymorphisms (RFLPs), Randomly Amplified Polymorphic DNAs (RAPDs),Arbitrarily Primed Polymerase Chain Reaction (AP-PCR), DNA AmplificationFingerprinting (DAF), Sequence Characterized Amplified Regions (SCARs),Amplified Fragment Length Polymorphisms (AFLPs), Simple Sequence Repeats(SSRs) and Single Nucleotide Polymorphisms (SNPs), may be used in plantbreeding methods utilizing XR31C09.

Isozyme Electrophoresis and RFLPs have been widely used to determinegenetic composition. Shoemaker and Olsen, ((1993) Molecular Linkage Mapof Soybean (Glycine max L. Merr.). p. 6.131-6.138. In S. J. O'Brien(ed.) Genetic Maps: Locus Maps of Complex Genomes. Cold Spring HarborLaboratory Press. Cold Spring Harbor, N.Y.), developed a moleculargenetic linkage map that consisted of 25 linkage groups with about 365RFLP, 11 RAPD (random amplified polymorphic DNA), three classicalmarkers, and four isozyme loci. See also, Shoemaker R. C. 1994 RFLP Mapof Soybean. P. 299-309 In R. L. Phillips and I. K. Vasil (ed.) DNA-basedmarkers in plants. Kluwer Academic Press Dordrecht, the Netherlands.

SSR technology is an efficient and practical marker technology; moremarker loci can be routinely used and more alleles per marker locus canbe found using SSRs in comparison to RFLPs. For example Diwan andCregan, described a highly polymorphic microsatellite loci in soybeanwith as many as 26 alleles. (Diwan, N., and P. B. Cregan 1997 Automatedsizing of fluorescent-labeled simple sequence repeat (SSR) markers toassay genetic variation in Soybean Theor. Appl. Genet. 95:220-225).Single Nucleotide Polymorphisms (SNPs) may also be used to identify theunique genetic composition of the invention and progeny varietiesretaining that unique genetic composition. Various molecular markertechniques may be used in combination to enhance overall resolution.

Soybean DNA molecular marker linkage maps have been rapidly constructedand widely implemented in genetic studies. One such study is describedin Cregan et. al, “An Integrated Genetic Linkage Map of the SoybeanGenome” Crop Science 39:1464-1490 (1999). Sequences and PCR conditionsof SSR Loci in Soybean as well as the most current genetic map may befound in Soybase on the world wide web.

One use of molecular markers is Quantitative Trait Loci (QTL) mapping.QTL mapping is the use of markers, which are known to be closely linkedto alleles that have measurable effects on a quantitative trait.Selection in the breeding process is based upon the accumulation ofmarkers linked to the positive effecting alleles and/or the eliminationof the markers linked to the negative effecting alleles from the plant'sgenome.

Molecular markers can also be used during the breeding process for theselection of qualitative traits. For example, markers closely linked toalleles or markers containing sequences within the actual alleles ofinterest can be used to select plants that contain the alleles ofinterest during a backcrossing breeding program. The markers can also beused to select for the genome of the recurrent parent and against thegenome of the donor parent. Using this procedure can minimize the amountof genome from the donor parent that remains in the selected plants. Itcan also be used to reduce the number of crosses back to the recurrentparent needed in a backcrossing program. The use of molecular markers inthe selection process is often called genetic marker enhanced selection.

Production of Double Haploids

The production of double haploids can also be used for the developmentof plants with a homozygous phenotype in the breeding program. Forexample, a soybean plant for which XR31C09 is a parent can be used toproduce double haploid plants. Double haploids are produced by thedoubling of a set of chromosomes (1 N) from a heterozygous plant toproduce a completely homozygous individual. For example, see Wan et al.,“Efficient Production of Doubled Haploid Plants Through ColchicineTreatment of Anther-Derived Maize Callus”, Theoretical and AppliedGenetics, 77:889-892, 1989 and US2003/0005479. This can be advantageousbecause the process omits the generations of selfing needed to obtain ahomozygous plant from a heterozygous source.

Methods for obtaining haploid plants are disclosed in Kobayashi, M. etal., Journ. of Heredity 71(1):9-14, 1980, Pollacsek, M., Agronomie(Paris) 12(3):247-251, 1992; Cho-Un-Haing et al., Journ. of Plant Biol.,1996, 39(3):185-188; Verdoodt, L., et al., February 1998, 96(2):294-300;Genetic Manipulation in Plant Breeding, Proceedings InternationalSymposium Organized by EUCARPIA, Sep. 8-13, 1985, Berlin, Germany;Chalyk et al., 1994, Maize Genet Coop. Newsletter 68:47; Chalyk, S.

Thus, an embodiment of this invention is a process for making asubstantially homozygous XR31C09 progeny plant by producing or obtaininga seed from the cross of XR31C09 and another soybean plant and applyingdouble haploid methods to the F1 seed or F1 plant or to any successivefilial generation. Based on studies in maize and currently beingconducted in soybean, such methods would decrease the number ofgenerations required to produce a variety with similar genetics orcharacteristics to XR31C09. See Bernardo, R. and Kahler, A. L., Theor.Appl. Genet. 102:986-992, 2001.

In particular, a process of making seed retaining the molecular markerprofile of soybean variety XR31C09 is contemplated, such processcomprising obtaining or producing F1 seed for which soybean varietyXR31C09 is a parent, inducing doubled haploids to create progeny withoutthe occurrence of meiotic segregation, obtaining the molecular markerprofile of soybean variety XR31C09, and selecting progeny that retainthe molecular marker profile of XR31C09.

Use Of XR31C09 In Tissue Culture

This invention is also directed to the use of variety XR31C09 in tissueculture. Tissue culture of various tissues of soybeans and regenerationof plants therefrom is well known and widely published. For example,reference may be had to Komatsuda, T. et al., “Genotype X SucroseInteractions for Somatic Embryogenesis in Soybean,” Crop Sci. 31:333-337(1991); Stephens, P. A. et al., “Agronomic Evaluation ofTissue-Culture-Derived Soybean Plants,” Theor. Appl. Genet. (1991)82:633-635; Komatsuda, T. et al., “Maturation and Germination of SomaticEmbryos as Affected by Sucrose and Plant Growth Regulators in SoybeansGlycine gracilis Skvortz and Glycine max (L.) Merr.,” Plant Cell, Tissueand Organ Culture, 28:103-113 (1992); Dhir, S. et al., “Regeneration ofFertile Plants from Protoplasts of Soybean (Glycine max L. Merr.):Genotypic Differences in Culture Response,” Plant Cell Reports (1992)11:285-289; Pandey, P. et al., “Plant Regeneration from Leaf andHypocotyl Explants of Glycine wightii (W. and A.) VERDC. var.longicauda,” Japan J. Breed. 42:1-5 (1992); and Shetty, K., et al.,“Stimulation of 1n Vitro Shoot Organogenesis in Glycine max (Merrill.)by Allantoin and Amides,” Plant Science 81:(1992) 245-251; as well asU.S. Pat. No. 5,024,944, issued Jun. 18, 1991 to Collins et al. and U.S.Pat. No. 5,008,200, issued Apr. 16, 1991 to Ranch et al., thedisclosures of which are hereby incorporated herein in their entirety byreference. Thus, another aspect of this invention is to provide cellswhich upon growth and differentiation produce soybean plants having thephysiological and morphological characteristics of soybean varietyXR31C09.

REFERENCES

-   Aukerman, M. J. et al. (2003) “Regulation of Flowering Time and    Floral Organ Identity by a MicroRNA and Its AP ETALA2-like Target    Genes” The Plant Cell 15:2730-2741-   Berry et al., Assessing Probability of Ancestry Using Simple    Sequence Repeat Profiles: Applications to Maize Inbred Lines and    Soybean Varieties” Genetics 165:331-342 (2003)-   Boppenmaier, et al., “Comparisons Among Strains of lnbreds for    RFLPs”, Maize Genetics Cooperative Newsletter, 65:1991, p. 90-   Conger, B. V., et al. (1987) “Somatic Embryogenesis From Cultured    Leaf Segments of Zea Mays”, Plant Cell Reports, 6:345-347-   Cregan et al, “An Integrated Genetic Linkage Map of the Soybean    Genome” Crop Science 39:1464-1490 (1999).-   Diwan et al., “Automated sizing of fluorescent-labeled simple    sequence repeat (SSR) markers to assay genetic variation in Soybean”    Theor. Appl. Genet. 95:220-225. (1997).-   Duncan, D. R., et al. (1985) “The Production of Callus Capable of    Plant Regeneration From Immature Embryos of Numerous Zea Mays    Genotypes”, Planta, 165:322-332-   Edallo, et al. (1981) “Chromosomal Variation and Frequency of    Spontaneous Mutation Associated with in Vitro Culture and Plant    Regeneration in Maize”, Maydica, XXVI:39-56-   Fehr, Walt, Principles of Cultivar Development, pp. 261-286 (1987)-   Green, et al. (1975) “Plant Regeneration From Tissue Cultures of    Maize”, Crop Science, Vol. 15, pp. 417-421-   Green, C. E., et al. (1982) “Plant Regeneration in Tissue Cultures    of Maize” Maize for Biological Research, pp. 367-372-   Hallauer, A. R. et al. (1988) “Corn Breeding” Corn and Corn    Improvement, No. 18, pp. 463-481-   Lee, Michael (1994) “Inbred Lines of Maize and Their Molecular    Markers”, The Maize Handbook, Ch. 65:423-432-   Meghji, M. R., et al. (1984) “Inbreeding Depression, Inbred & Hybrid    Grain Yields, and Other Traits of Maize Genotypes Representing Three    Eras”, Crop Science, Vol. 24, pp. 545-549-   Openshaw, S. J., et al. (1994) “Marker-assisted selection in    backcross breeding”. pp. 41-43. In Proceedings of the Symposium    Analysis of Molecular Marker Data. 5-7 Aug. 1994. Corvallis, Oreg.,    American Society for Horticultural Science/Crop Science Society of    America-   Phillips, et al. (1988) “Cell/Tissue Culture and In Vitro    Manipulation”, Corn & Corn Improvement, 3rd Ed., ASA Publication,    No. 18, pp. 345-387-   Poehlman et al (1995) Breeding Field Crop, 4th Ed., Iowa State    University Press, Ames, Iowa., pp. 132-155 and 321-344-   Rao, K. V., et al., (1986) “Somatic Embryogenesis in Glume Callus    Cultures”, Maize Genetics Cooperative Newsletter, No. 60, pp. 64-65-   Sass, John F. (1977) “Morphology”, Corn & Corn Improvement, ASA    Publication, Madison, Wis. pp. 89-109-   Smith, J. S. C., et al., “The Identification of Female Selfs in    Hybrid Maize: A Comparison Using Electrophoresis and Morphology”,    Seed Science and Technology 14, 1-8-   Songstad, D. D. et al. (1988) “Effect of    ACC(1-aminocyclopropane-1-carboyclic acid), Silver Nitrate &    Norbonadiene on Plant Regeneration From Maize Callus Cultures”,    Plant Cell Reports, 7:262-265-   Tomes, et al. (1985) “The Effect of Parental Genotype on Initiation    of Embryogenic Callus From Elite Maize (Zea Mays L.) Germplasm”,    Theor. Appl. Genet., Vol. 70, p. 505-509-   Troyer, et al. (1985) “Selection for Early Flowering in Corn: 10    Late Synthetics”, Crop Science, Vol. 25, pp. 695-697-   Umbeck, et al. (1983) “Reversion of Male-Sterile T-Cytoplasm Maize    to Male Fertility in Tissue Culture”, Crop Science, Vol. 23, pp.    584-588-   Wan et al., “Efficient Production of Doubled Haploid Plants Through    Colchicine Treatment of Anther-Derived Maize Callus”, Theoretical    and Applied Genetics, 77:889-892, 1989-   Wright, Harold (1980) “Commercial Hybrid Seed Production”,    Hybridization of Crop Plants, Ch. 8:161-176-   Wych, Robert D. (1988) “Production of Hybrid Seed”, Corn and Corn    Improvement, Ch. 9, pp. 565-607

DEPOSITS

Applicant made a deposit of seeds of Soybean Variety XR31C09 with theAmerican Type Culture Collection (ATCC), Manassas, Va. 20110 USA, ATCCDeposit No. PTA-11525. The seeds deposited with the ATCC on Dec. 7, 2010were be taken from the seed stock maintained by Pioneer Hi-BredInternational, Inc., 7250 NW 62^(nd) Avenue, Johnston, Iowa 50131 sinceprior to the filing date of this application. Access to this seed stockwill be available during the pendency of the application to theCommissioner of Patents and Trademarks and persons determined by theCommissioner to be entitled thereto upon request. Upon allowance of anyclaims in the application, the Applicant will make the deposit availableto the public pursuant to 37 C.F.R. §1.808. This deposit of SoybeanVariety XR31C09 will be maintained in the ATCC depository, which is apublic depository, for a period of 30 years, or 5 years after the mostrecent request, or for the enforceable life of the patent, whichever islonger, and will be replaced if it becomes nonviable during that period.Additionally, Applicant has or will satisfy all the requirements of 37C.F.R. §§1.801-1.809, including providing an indication of the viabilityof the sample upon deposit. Applicant has no authority to waive anyrestrictions imposed by law on the transfer of biological material orits transportation in commerce. Applicant does not waive anyinfringement of their rights granted under this patent or under thePlant Variety Protection Act (7 USC 2321 et seq.).

TABLE 1 Variety Description Information for XR31C09 Current Variety NameXR31C09 Relative Maturity 3.1 Herbicide Resistance Glyphosate ResistanceYield Potential Harvest Standability Field Emergence Hypocotyl LengthPhytophthora Gene Phytophthora Race 5 Phytophthora Race 7 PhytophthoraRace 25 Phytophthora Field Tolerance Brown Stem Rot Iron Chlorosis WhiteMold Tolerance Sudden Death Syndrome Cyst Nematode Race 1 Cyst NematodeRace 2 Cyst Nematode Race 3 Cyst Nematode Race 5 Cyst Nematode Race 14Aphid Antibiosis 7 Root-knot Nematode - Southern Root-knot Nematode -Peanut Stem Canker Genetic Stem Canker Tolerance Frogeye Leaf SpotAerial Web Blight Chloride Sensitivity Canopy Width Shattering PlantHabit Ind Oil/Meal Type HLC, LLC Seed Protein (% @ 13% H20) Seed Oil (%@ 13% H20) Seed Size Score 6 Seed Size Range (avg seeds/lb) Flower ColorW Pubescence Color L Hila Color BL Pod Color BR Seed Coat Luster D

TABLE 2 VARIETY COMPARISON DATA YIELD bu/a MAT ABS LDG SEV Variety1Variety2 Statistic 60# ABS countABS HGT in ABS score ABS XR31C09 93M11Mean1 53.7 125.1 36.4 5 XR31C09 93M11 Mean2 52 124.2 31.4 8 XR31C0993M11 #Locs 26 12 5 6 XR31C09 93M11 #Reps 28 13 5 6 XR31C09 93M11 #Years2 2 1 2 XR31C09 93M11 % Wins 53.8 66.7 0 0 XR31C09 93M11 Diff 1.8 1 −5−3 XR31C09 93M11 SE Diff 1 0.42 0.32 0.6 XR31C09 93M11 Prob 0.091 0.04320 0.005 XR31C09 93M42 Mean1 52.4 125.4 36.4 6 XR31C09 93M42 Mean2 51.4130.2 35.8 7 XR31C09 93M42 #Locs 22 10 5 5 XR31C09 93M42 #Reps 23 11 5 5XR31C09 93M42 #Years 1 1 1 1 XR31C09 93M42 % Wins 50 0 60 0 XR31C0993M42 Diff 1 −4.8 −0.6 −1 XR31C09 93M42 SE Diff 1.31 0.64 1.29 0.6XR31C09 93M42 Prob 0.449 0 0.67 0.109 XR31C09 93Y10 Mean1 52.4 125.436.4 6 XR31C09 93Y10 Mean2 50.6 124.6 32.8 7 XR31C09 93Y10 #Locs 22 10 55 XR31C09 93Y10 #Reps 23 11 5 5 XR31C09 93Y10 #Years 1 1 1 1 XR31C0993Y10 % Wins 63.6 60 0 0 XR31C09 93Y10 Diff 1.7 0.8 −3.6 −2 XR31C0993Y10 SE Diff 1.16 0.39 0.87 0.7 XR31C09 93Y10 Prob 0.151 0.0697 0.010.078 XR31C09 93Y11 Mean1 52.4 125.4 36.4 6 XR31C09 93Y11 Mean2 50.8126.1 33.2 7 XR31C09 93Y11 #Locs 22 10 5 5 XR31C09 93Y11 #Reps 23 11 5 5XR31C09 93Y11 #Years 1 1 1 1 XR31C09 93Y11 % Wins 50 30 0 0 XR31C0993Y11 Diff 1.5 −0.7 −3.2 −2 XR31C09 93Y11 SE Diff 1.62 0.54 0.8 0.4XR31C09 93Y11 Prob 0.35 0.2259 0.02 0.009 XR31C09 93Y20 Mean1 52.4 125.436.4 6 XR31C09 93Y20 Mean2 52.8 126 36.4 6 XR31C09 93Y20 #Locs 22 10 5 5XR31C09 93Y20 #Reps 24 11 5 5 XR31C09 93Y20 #Years 1 1 1 1 XR31C09 93Y20% Wins 45.5 20 40 20 XR31C09 93Y20 Diff −0.4 −0.6 0 −1 XR31C09 93Y20 SEDiff 0.97 0.45 1.26 0.9 XR31C09 93Y20 Prob 0.666 0.2172 1 0.405 SDSscore PROTN pct OIL PCT pct Variety1 Variety2 Statistic ABS ABS ABS R160pct ABS XR31C09 93M11 Mean1 5.5 34.5 18.3 7.36 XR31C09 93M11 Mean2 5.932.7 19.9 9.78 XR31C09 93M11 #Locs 4 19 19 20 XR31C09 93M11 #Reps 6 1919 20 XR31C09 93M11 #Years 1 1 1 2 XR31C09 93M11 % Wins 25 89.5 10.5 100XR31C09 93M11 Diff −0.4 1.83 −1.6 2.42 XR31C09 93M11 SE Diff 0.55 0.430.21 0.2 XR31C09 93M11 Prob 0.547 0 0 0 XR31C09 93M42 Mean1 5.5 34.618.3 7.46 XR31C09 93M42 Mean2 6.8 33.6 17.8 10.6 XR31C09 93M42 #Locs 418 18 18 XR31C09 93M42 #Reps 6 18 18 18 XR31C09 93M42 #Years 1 1 1 1XR31C09 93M42 % Wins 0 83.3 77.8 100 XR31C09 93M42 Diff −1.3 0.97 0.513.13 XR31C09 93M42 SE Diff 0.75 0.34 0.2 0.21 XR31C09 93M42 Prob 0.1940.01 0.02 0 XR31C09 93Y10 Mean1 5.5 34.5 18.3 7.43 XR31C09 93Y10 Mean2 731.2 20.5 9.56 XR31C09 93Y10 #Locs 4 19 19 19 XR31C09 93Y10 #Reps 6 1919 19 XR31C09 93Y10 #Years 1 1 1 1 XR31C09 93Y10 % Wins 0 89.5 5.26 100XR31C09 93Y10 Diff −1.5 3.36 −2.1 2.14 XR31C09 93Y10 SE Diff 0.54 0.420.22 0.21 XR31C09 93Y10 Prob 0.069 0 0 0 XR31C09 93Y11 Mean1 5.5 34.518.3 7.34 XR31C09 93Y11 Mean2 8.3 34.1 19.1 10.1 XR31C09 93Y11 #Locs 419 19 18 XR31C09 93Y11 #Reps 6 19 19 18 XR31C09 93Y11 #Years 1 1 1 1XR31C09 93Y11 % Wins 0 79 10.5 100 XR31C09 93Y11 Diff −2.8 0.47 −0.82.74 XR31C09 93Y11 SE Diff 0.48 0.38 0.21 0.22 XR31C09 93Y11 Prob 0.0110.23 0 0 XR31C09 93Y20 Mean1 5.5 34.5 18.3 7.43 XR31C09 93Y20 Mean2 7.332.6 19.2 9.29 XR31C09 93Y20 #Locs 4 19 19 19 XR31C09 93Y20 #Reps 6 1919 19 XR31C09 93Y20 #Years 1 1 1 1 XR31C09 93Y20 % Wins 0 84.2 10.5 100XR31C09 93Y20 Diff −1.8 1.93 −0.9 1.87 XR31C09 93Y20 SE Diff 0.25 0.350.2 0.2 XR31C09 93Y20 Prob 0.006 0 0 0 R180 pct R181 pct R182 pct R183pct Variety1 Variety2 Statistic ABS ABS ABS ABS XR31C09 93M11 Mean1 4.4467.8 17.4 2.88 XR31C09 93M11 Mean2 4.91 24.5 53.4 7.39 XR31C09 93M11#Locs 20 20 20 20 XR31C09 93M11 #Reps 20 20 20 20 XR31C09 93M11 #Years 22 2 2 XR31C09 93M11 % Wins 95 0 100 100 XR31C09 93M11 Diff 0.47 −43 364.51 XR31C09 93M11 SE Diff 0.09 2.64 2.39 0.11 XR31C09 93M11 Prob 0 0 00 XR31C09 93M42 Mean1 4.44 66.3 18.6 2.98 XR31C09 93M42 Mean2 5.35 26.650.1 7.23 XR31C09 93M42 #Locs 18 18 18 18 XR31C09 93M42 #Reps 18 18 1818 XR31C09 93M42 #Years 1 1 1 1 XR31C09 93M42 % Wins 100 0 100 100XR31C09 93M42 Diff 0.91 −40 31.5 4.24 XR31C09 93M42 SE Diff 0.12 2.642.36 0.09 XR31C09 93M42 Prob 0 0 0 0 XR31C09 93Y10 Mean1 4.47 66.9 18.12.94 XR31C09 93Y10 Mean2 4.69 23.3 54.8 7.52 XR31C09 93Y10 #Locs 19 1919 19 XR31C09 93Y10 #Reps 19 19 19 19 XR31C09 93Y10 #Years 1 1 1 1XR31C09 93Y10 % Wins 84.2 0 100 100 XR31C09 93Y10 Diff 0.22 −44 36.74.58 XR31C09 93Y10 SE Diff 0.1 2.72 2.46 0.14 XR31C09 93Y10 Prob 0.03 00 0 XR31C09 93Y11 Mean1 4.45 67.7 17.5 2.92 XR31C09 93Y11 Mean2 4.4224.2 53.7 7.5 XR31C09 93Y11 #Locs 18 18 18 18 XR31C09 93Y11 #Reps 18 1818 18 XR31C09 93Y11 #Years 1 1 1 1 XR31C09 93Y11 % Wins 50 0 100 100XR31C09 93Y11 Diff −0 −43 36.2 4.58 XR31C09 93Y11 SE Diff 0.1 2.66 2.390.15 XR31C09 93Y11 Prob 0.73 0 0 0 XR31C09 93Y20 Mean1 4.47 66.9 18.12.94 XR31C09 93Y20 Mean2 4.23 22.9 55.9 7.65 XR31C09 93Y20 #Locs 19 1919 19 XR31C09 93Y20 #Reps 19 19 19 19 XR31C09 93Y20 #Years 1 1 1 1XR31C09 93Y20 % Wins 36.8 0 100 100 XR31C09 93Y20 Diff −0.2 −44 37.84.71 XR31C09 93Y20 SE Diff 0.08 2.7 2.42 0.12 XR31C09 93Y20 Prob 0.01 00 0

TABLE 3 Soybean SSR Marker Set SAC1006 SATT129 SATT243 SATT334 SAC1611SATT130 SATT247 SATT335 SAC1634 SATT131 SATT249 SATT336 SAC1677 SATT133SATT250 SATT338 SAC1699 SATT142 SATT251 SATT339 SAC1701 SATT144 SATT255SATT343 SAC1724 SATT146 SATT256 SATT346 SAT_084 SATT147 SATT257 SATT347SAT_090 SATT150 SATT258 SATT348 SAT_104 SATT151 SATT259 SATT352 SAT_117SATT153 SATT262 SATT353 SAT_142-DB SATT155 SATT263 SATT355 SAT_189SATT156 SATT264 SATT356 SAT_222-DB SATT165 SATT265 SATT357 SAT_261SATT166 SATT266 SATT358 SAT_270 SATT168 SATT267 SATT359 SAT_271-DBSATT172 SATT270 SATT361 SAT_273-DB SATT175 SATT272 SATT364 SAT_275-DBSATT181 SATT274 SATT367 SAT_299 SATT183 SATT279 SATT369 SAT_301 SATT186SATT280 SATT373 SAT_311-DB SATT190 SATT282 SATT378 SAT_317 SATT191SATT284 SATT380 SAT_319-DB SATT193 SATT285 SATT383 SAT_330-DB SATT195SATT287 SATT385 SAT_331-DB SATT196 SATT292 SATT387 SAT_343 SATT197SATT295 SATT389 SAT_351 SATT199 SATT299 SATT390 SAT_366 SATT202 SATT300SATT391 SAT_381 SATT203 SATT307 SATT393 SATT040 SATT204 SATT314 SATT398SATT042 SATT212 SATT319 SATT399 SATT050 SATT213 SATT321 SATT406 SATT092SATT216 SATT322 SATT409 SATT102 SATT219 SATT326 SATT411 SATT108 SATT221SATT327 SATT412 SATT109 SATT225 SATT328 SATT413 SATT111 SATT227 SATT330SATT414 SATT115 SATT228 SATT331 SATT415 SATT122 SATT230 SATT332 SATT417SATT127 SATT233 SATT333 SATT418 SATT420 SATT508 SATT583 SATT701 SATT421SATT509 SATT584 SATT708-TB SATT422 SATT510 SATT586 SATT712 SATT423SATT511 SATT587 SATT234 SATT429 SATT512 SATT590 SATT240 SATT431 SATT513SATT591 SATT242 SATT432 SATT514 SATT594 SATT433 SATT515 SATT595 SATT436SATT517 SATT596 SATT440 SATT519 SATT597 SATT441 SATT522 SATT598 SATT442SATT523 SATT601 SATT444 SATT524 SATT602 SATT448 SATT526 SATT608 SATT451SATT529 SATT613 SATT452 SATT533 SATT614 SATT454 SATT534 SATT617 SATT455SATT536 SATT618 SATT457 SATT537 SATT628 SATT460 SATT540 SATT629 SATT461SATT544 SATT630 SATT464 SATT545 SATT631 SATT466 SATT546 SATT632-TBSATT467 SATT548 SATT633 SATT469 SATT549 SATT634 SATT470 SATT550 SATT636SATT471 SATT551 SATT640-TB SATT473 SATT552 SATT651 SATT475 SATT555SATT654 SATT476 SATT556 SATT655-TB SATT477 SATT557 SATT656 SATT478SATT558 SATT660 SATT479 SATT565 SATT661-TB SATT480 SATT566 SATT662SATT487 SATT567 SATT665 SATT488 SATT568 SATT666 SATT491 SATT569 SATT667SATT492 SATT570 SATT672 SATT493 SATT572 SATT675 SATT495 SATT573 SATT677SATT497 SATT576 SATT678 SATT503 SATT578 SATT680 SATT506 SATT581 SATT684SATT507 SATT582 SATT685

All publications, patents and patent applications mentioned in thespecification are indicative of the level of those skilled in the art towhich this invention pertains. All such publications, patents and patentapplications are incorporated by reference herein for the purpose citedto the same extent as if each was specifically and individuallyindicated to be incorporated by reference herein.

The foregoing invention has been described in detail by way ofillustration and example for purposes of clarity and understanding. Asis readily apparent to one skilled in the art, the foregoing are onlysome of the methods and compositions that illustrate the embodiments ofthe foregoing invention. It will be apparent to those of ordinary skillin the art that variations, changes, modifications and alterations maybe applied to the compositions and/or methods described herein withoutdeparting from the true spirit, concept and scope of the invention.

1. A plant or plant part of soybean variety XR31C09, representative seedof said soybean variety XR31C09 having been deposited under ATCCAccession Number PTA-11525.
 2. A seed of the soybean variety of claim 1.3. The seed of claim 2, further comprising a transgene.
 4. The seed ofclaim 3, wherein the transgene confers a trait selected from the groupconsisting of male sterility, site-specific recombination, abioticstress tolerance, altered phosphorus, altered antioxidants, alteredfatty acids, altered essential amino acids, altered carbohydrates,herbicide resistance, insect resistance and disease resistance.
 5. Asoybean plant, or a part thereof, produced by growing the seed of claim2.
 6. A tissue culture produced from protoplasts or regenerable cellsfrom the plant of claim
 5. 7. A method for developing a second soybeanplant in a soybean plant breeding program comprising applying plantbreeding techniques to a first soybean plant, or parts thereof, whereinsaid first soybean plant is the soybean plant of claim 5, and whereinapplication of said techniques results in development of said secondsoybean plant.
 8. A method for producing soybean seed comprisingcrossing two soybean plants and harvesting the resultant soybean seed,wherein at least one soybean plant is the soybean plant of claim
 5. 9.The soybean seed produced by the method of claim
 8. 10. A soybean plant,or a part thereof, produced by growing said seed of claim
 9. 11. Amethod for developing a second soybean plant in a soybean plant breedingprogram comprising applying plant breeding techniques to a first soybeanplant, or parts thereof, wherein said first soybean plant is the soybeanplant of claim 10, and wherein application of said techniques results indevelopment of said second soybean plant.
 12. A method of producing asoybean plant comprising a locus conversion, the method comprisingintroducing a locus conversion into the plant of claim 5, wherein saidlocus conversion confers a trait selected from the group consisting ofmale sterility, site-specific recombination, abiotic stress tolerance,altered phosphorus, altered antioxidants, altered fatty acids, alteredessential amino acids, altered carbohydrates, herbicide resistance,insect resistance and disease resistance.
 13. An herbicide resistantsoybean plant produced by the method of claim
 12. 14. A diseaseresistant soybean plant produced by the method of claim
 12. 15. Aninsect resistant soybean plant produced by the method of claim
 12. 16.The soybean plant of claim 15, wherein the locus conversion comprises atransgene encoding a Bacillus thuringiensis (Bt) endotoxin.
 17. Theplant of claim 5, further comprising a transgene.
 18. The plant of claim17, wherein the transgene confers a trait selected from the groupconsisting of male sterility, site-specific recombination, abioticstress tolerance, altered phosphorus, altered antioxidants, alteredfatty acids, altered essential amino acids, altered carbohydrates,herbicide resistance, insect resistance and disease resistance.
 19. Amethod for developing a second soybean plant in a soybean plant breedingprogram comprising applying plant breeding techniques to a first soybeanplant, or parts thereof, wherein said first soybean plant is the soybeanplant of claim 17, and wherein application of said techniques results indevelopment of said second soybean plant.
 20. A soybean plant, or a partthereof, expressing all the physiological and morphologicalcharacteristics of soybean variety XR31C09, representative seed of saidsoybean variety XR31C09 having been deposited under ATCC AccessionNumber PTA-11525.